I have a '98 4Runner,manual transmission. Can't set cruise control unless I push the brake pedal up hard from the bottom. How do I adjust the brake pedal so cruise works?

Your best bet , take your vehicle to a qualified repair shop that has a professional scan tool an service repair info . So it can be diagnosed correctly . The Stop lamp switch is not a old school conventional type . Has three wires , five volt ref. voltage from the BCM ,
Stop Lamps
The brake pedal position sensor is used to sense the action of the driver application of the brake pedal. The brake pedal position sensor provides an analog voltage signal that will increase as the brake pedal is applied. The body control module (BCM) provides a low reference signal and a 5-volt reference voltage to the brake pedal position sensor. When the variable signal reaches a voltage threshold indicating the brakes have been applied, the BCM will apply battery positive voltage to the stop lamps, center high mounted stop lamp (CHMSL), transmission control module (TCM), and engine control module (ECM). Ground for the right rear stop lamp and CHMSL is applied at G402. Ground for the left rear stop lamp is applied at G400. The stop lamps on this vehicle will not illuminate unless the ignition is in the accessory, run, or crank positions. When the ignition is in the OFF position the stop lamps will not illuminate when the brake pedal is applied.

Checking for DTC's - diagnostic trouble code's in the BCM would be my first diagnostic step , not guessing an replacing parts .

DTC B3903 02: Stop Lamp Relay Circuit Short to Ground
DTC B3903 05: Stop Lamp Relay Circuit Open or Short to Voltage

DTC C0277 06: Brake Pedal Position Sensor Circuit Short to Ground or Open
DTC C0277 07 : Brake Pedal Position Sensor Circuit Voltage Above Threshold
DTC C0277 09 : Brake Pedal Position Sensor Circuit Rate of Change Above Threshold

DTC C0278 00: Brake Pedal Position Sensor Not Calibrated

DTC C0870 03 : Device Voltage Reference Output 1 Circuit Voltage Below Threshold
DTC C0870 07 : Device Voltage Reference Output 1 Circuit Voltage Above Threshold
As you can see a number of DTC'S can be set , so do yourself a favor an let a qualified technician check it

Circuit/System Description
The brake pedal position sensor is used to sense the action of the driver application of the brake pedal. The brake pedal position sensor provides an analog voltage signal that will increase as the brake pedal is applied. The body control module (BCM) provides a low reference signal and a 5-volt reference voltage to the brake pedal position sensor. When the variable signal reaches a voltage threshold indicating the brakes have been applied, the BCM will apply battery positive voltage to the stop lamps, center high mounted stop lamp (CHMSL), transmission control module (TCM), and engine control module (ECM). The stop lamps will not operate unless the ignition is in the ON position.

DTC P0572 : Brake Switch Circuit 1 Low Voltage
DTC P0573 : Brake Switch Circuit 1 High Voltage

It's hard to fix something when you don't have a clue how it works . The CC is also a controlled function of the BCM .
The BCM monitors the signal circuit of the cruise control switches. The BCM relays the cruise control switch status to the ECM via the GMLAN serial data circuit. The ECM uses the status of the cruise control switch to determine when to capture and maintain the vehicle speed. The ECM monitors the vehicle speed signal circuit in order to determine and the desired vehicle speed. The ECM uses the TAC motor in order to maintain the vehicle speed. For further review of the TAC system, refer to Throttle Actuator Control (TAC) System Description for the 2.0L engine or to Throttle Actuator Control (TAC) System Description for the 2.4L engine. Ignition voltage is supplied to the cruise control switch from the 2-amp CRUISE fuse located in the integrated BCM fuse block. The cruise control switches are located on the steering wheel. The cruise control function switches are arranged in a resistive ladder design, with each cruise control function switch having a different resistance value. The BCM detects a specific voltage value that is associated with any cruise control function switch being activated. When the normally open cruise control on/off switch is turned ON, the switch closes and the BCM detects a predetermined voltage signal on the cruise control set/coast and resume/accel switch signal circuit. The BCM sends a GMLAN serial data message to the ECM indicating that the On/Off switch is active. Similarly, when the + RES switch or the - SET switch are pressed, the BCM detects the predetermined voltage signal on the cruise control set/coast and resume/accel switch signal circuit. To engage the cruise control system, ensure that the vehicle speed is above 40.2 km/h (25 mph), turn the cruise On/Off switch ON and momentarily press the - SET switch. The ECM will engage the cruise control system and record the vehicle speed. The ECM sends a GMLAN serial data message via the BCM to the driver information center (DIC) in order to display the CRUISE ENGAGED message. The - SET switch or the + RES switch will remain inactive when the BCM has not received the predetermined voltage signal from the On/Off switch. Pressing the accelerator pedal, while the cruise control system is engaged, will allow the driver to override the cruise control system in order to accelerate the vehicle beyond the current set vehicle speed. When the accelerator pedal is released, the vehicle will decelerate and resume the current set vehicle speed. The driver can also override the current set vehicle speed via the - SET switch and the + RES switch. When the cruise control system is engaged, pressing and holding the - SET switch will allow the vehicle to decelerate from the current set vehicle speed without deactivating the cruise control system. When the - SET switch is released, the ECM will record the vehicle speed and maintain the vehicle speed as the new set vehicle speed. When the cruise control system is engaged, momentarily pressing the - SET switch will allow the vehicle to decelerate at 1.6 km/h (1 mph) increments for each time that the - SET is momentarily pressed, with a minimum vehicle speed of 37 km/h (23 mph). Pressing and holding the + RES switch, when the cruise control system is engaged, will allow the vehicle to accelerate to a greater vehicle speed than the current set vehicle speed. When the + RES switch is released, the ECM will record the vehicle speed and maintain the vehicle speed as the new set vehicle speed. When the cruise control system is engaged, momentarily pressing the + RES switch will allow the vehicle to accelerate at 1.6 km/h (1 mph) increments for each time that the + RES switch is momentarily pressed, with the maximum acceleration total of 16 km/h (10 mph) over the current set vehicle speed. Momentarily pressing the + RES switch after the cruise control system has been disengaged by pressing the brake pedal, will recall the previous set vehicle speed that is recorded in the ECM.

Most common problem is the brake "kick out" switch gets knocked out of position or adjustment. It must be pushed in when brake pedal is up, in order for cruise to engage.

Alarmingly, the speedometer needle steadily winds down from 75 mph toward 50. Just as you uncurl your feet and try to accelerate back to traffic speeds, the vehicle downshifts with a lurch and abruptly climbs back to over 80 mph. So you tap the brakes and disengage the cruise control to avoid a conversation with one of the many law enforcement officers lurking behind every other billboard. Toggling the Resume switch settles things down, holding to a legal speed on both the uphill and downhill sections of the interstate. The kids in the back seat have stopped threatening to throw up, too. Then you look in your mirror 20 miles later and see the lights. Red and blue flashing lights. You're doing over 85 mph and, odds are, Smokey isn't going to believe you have the cruise set to 70. Time to find out why your cruise control has a mind of its own.
IT'S NOT A BUG, IT'S A FEATURE
Does your cruise control fall out of engagement partway up steep hills? Actually, it will normally drop out if the engine has to work too hard, mainly because after a while there isn't enough vacuum left to pull in the servo after sustained near-wide-open-throttle. You'll just have to put your foot into it. Downshifting helps. Do you have to ride the brakes on longer downhills to keep from building up excess speed? That's normal too. The cruise control only has authority to reduce engine speed to idle. It doesn't activate the brakes. Modern cars, in an attempt to improve mileage, have very tall gear ratios, low-friction engine designs, low-rolling-resistance tires and optimized aerodynamics. That long downgrade outside of town may have accelerated your '60s-era Pontiac to only a couple of miles per hour above legal. But, it may well propel your new economy car to blatantly ******* velocities unless you intervene by braking or downshifting. Does the Cruise icon on the dash light up when you turn the switch on? Duh. Check the fuse. You may need to look in the owner's manual to see which one if it's not tagged on the fuse box cover. An aftermarket cruise may have an inline fuse holder in the wiring to the controller.
If there is power to the system, the next check is the brake lights. Brake lights? Yup, cruise controls have a switch to toggle them off when you touch the brake pedal, and many use the same switch as the brake lights. If one of the brake lights has failed, the cruise control thinks the brakes are on all the time and won't come on. Same result if the switch is incorrectly adjusted or broken or jammed. Wait, there's more--if your vehicle has a manual transmission, there's a similar switch on the clutch pedal. You may need to break out a test light or multimeter to verify the function of this array of switches. These switches usually are normally closed switches, and close their contacts when the pedal is depressed. We've seen several cases of intermittent cruise control dropout caused by a brake light switch that was adjusted very tight. Any small bump would jiggle the brake pedal down far enough to toggle the brake lights on for a brief instant--long enough to shut down the cruise. Adjusting the switch to specs (usually so the brake lights come on after the pedal travels 1/2 in.) fixed it.

cruise controls are governed by 5 settings and sensors
one is engine rpms
vehicle road speed ,( manual transmission will not activate under 20 klms /hr
brake pedal switch
clutch pedal switch ( VSS if auto)
off/on switch control
any one of these not lined up will not allow the cruise control to work

• Brake Switch (Cruise Control) Clutch Switch
  
• Cruise Control Module
• Cruise Control Servo Cruise Control Switch
  
• Release Valve
• Vacuum Pump
• Vacuum Vent ValveVacuum System, Checking For Leaks
  • Remove vacuum hose from vacuum pump seal off.
  • Remove lower instrument panel cover, left.
  • Push servo unit diaphragm in, to do this press brake pedal down by hand until pressure point.
  • Then release brake pedal.
  The diaphragm must not move.
  
  NOTE: Malfunctions can be caused by an incorrectly adjusted vent valve, leaking servo unit or through cracks in the vacuum hoses.Here is a quick run down of the components I need more info to help u more is ur car a syncro or a sedan is ur engine a 1.8, 1.9 or 2.8
  

There are two switches on the brake pedal, one for brake light, and one that kicks out the cruise when you hit the brake. That switch is closed when depressed (ie; brake pedal is up) and opens when pedal is pushed away from the switch, (unlike the brake light switch which closes when the pedal is pushed). This means it must be positioned and adjusted correctly for cruise to work.

Check your fuse panels both inside, and outside the vehicle, as well as the connections to the cruise control.

You'll need to repace the switch itself if it is defective. These are available at most auto-parts stores, and looking at the switch itself will help in determining what you actually need to do in removing it. It fits into a set position on the side of the dash nearest to the driver, just in front of the brake pedal arm, and is operated by pressing on the brake pedal, which causes the switch to make contact internally and pass voltage through to the brake light or to the cruise control system.

To remove, disconnect wiring harness, remove the front retaining nut and once it's removed, slide the switch out of the mount, just compare the new switch to the old one to make sure they are the same, then reinstall after putting the nuts & washers at approximately the same location on the new one, once installed, test the adjustment by making sure the brake light is not on without the brake pedal being pushed, then check the cruise control, it should engage properly as well as disengage when you press on the brake pedal. Adjustments are made by adjusting the mounting position either forwards or backwards with the mounting hardware.

If you are having problems with this, verify the voltage coming into one side of the switch with the pedal not being pressed, then the voltage should pass through the switch, when the brake pedal is pressed. On a dual switch (see below) ground voltage goes through the Cruise control part of the switch-depending on the model, but on either type, removing the connection from the switch and verifying continuity when the switch is activated will determine if it is working properly, as long as the switch breaks continuity when not being activated.

Some of these switches are dual purpose, working both the brake light and the cruise control, some are individual switches with one for each, and on some cars, the brake light switch works for both the cruise and the brake light.

Good luck.

Lift the pedal, and see if the light goes off, if it does, there is a switch on the pedal that is out of adjustment. If it does not go off, the switch could have fallen off, or it is broken. Anyways, it is under the dash, should be right up the brake pedal. First, try to adjust it, to get it closer to the brake pedal arm, if it doesn't go off, it should be bad, take it off, and take it to the auto parts place, they should be able to test it, with a multimeter.
This is probably why the cruise control does not work also, as when you drive down the road and hit the brakes, the cruise goes off.

Not sure, but your brake pedal might not be pushing the brake light switch back in. Next time it happens, stop somewhere safe, put the car in park and check the brake lights on the rear of the vehicle with nobody's foot on the brake pedal. If they're still on, try pulling the brake pedal up with your foot and check to see if the lights go off. If they are on then go off, you can usually adjust the brake switch closer to the pedal to put more pressure on it to get the lights to go off. If not, you might have to get a new switch. If that's not it, try wiggling the wires with it in park then take off again and see if it'll return to cruise control.