2004 Jeep Wrangler cleaning out cats...Will this make the motor run bad???

Hesitation is usually a dirty throttle body and idle air control motor.

There are fusible links which could fail, usually in the wiring from the battery + or located near the starter motor. Also possible you have a bad light switch. Use a voltmeter to find this.

You can run without a thermostat in the summer time but not in the Winter time

was the computer programed??, also how about the crank sensor, then the next thing is to check for a bad cat, you may have a clogged cat converter that restricks the exhaust flow,and last is the o2 sensor. have your computer scanned for any codes.

The jeep has air injection and this is part of the air pump. The cat should have two ports.. These tubes should have check valves to prevent backfire.Usually their routed up on both sides of motor and attached at the air cleaner abouts

There are several things you can do if you haven't done so already, Check voltage at ignition coil, as soon as the engine starts to turn over there should be voltage. If not, the crank sensor is not triggering the ECM quickly.... on 98-99 wranglers, this was a problem area. Check terminal connectors at the ECM, clean and secure, another area of concern.The module on the side of the throttle body is the air idle control 'motor' as jeep calls it. Over time they tend to carbon up and it results in bad air/fuel mixture and yet fails to send a fault code, you can remove & clean also the O2 sensor in front of the cat. convertor.remove & clean. Check fuel pressure, you should have some residual PSI. Treat fuel system with a good treatment...I like the Lucas products, their fuel system treatment and injector cleaner burns hot & clean.
I hope these suggestions help...and the wrangler returns to top form...good luck.

The blower motor squirrel cage blower wheel must be rubbing inside the blower case or something is in there like leaves..

IF ITS A 4.0 L THE THROTTLE BODY MAY JUST NEED TO BE CLEANED, AS FOR A SENSOR ITS POSSIBLE BOTH THE CAM AND CRANK SENSORS ARE GARBAGE ON THAT VEHICLE I CHANGE THEM ALL THE TIME

THE SOLINOID VALVE IS ONLY PART OF THE SYSTEM YOU MAY HAVE A LDP (LEAK DETECTION PUMP) PROBLEM INTERNAL LEAKS ARE HARD TO DIAG YOU MAY WANT TO BRING TO A DEALER.

Clean the inside of the MAF sensor with MAF sensor spray, it is made bt CRC.