What is the proper way to wire up alternator

Sounds like the wiring might not have been hooked up properly, so the new alternator isn't charging the battery. Alternators have one BIG wire direct to the battery, and one or more smaller wires that connect at a different location, and it's easy to forget about the smaller ones.
Also possible that either the new battery or the new alternator is bad (doesn't charge, has bad diodes allowing battery to discharge). Auto parts stores will test both for free, so if you can't find a wiring problem, take 'em out for testing.

alternator or associated wiring suspect... test for 14.4 volts at battery when all is hooked up proper and running.. if less replace alternator or diagnose further the wiring to and from alternator

http://binatani.com/wp-content/uploads/2011/08/International-Harvester-Farmall-M-alternator-conversion-schematic.jpg

Wire it following the recommendation of the manufacturer of the alternator. Google is your friend....

Well, according to my diagrams for 88-94 models, the alternator only uses the red and brown. There are pink-black wires that power some of the sensors and solenoids but should go to a fuse marked ECM in the fuse box.
Have you tried hooking up the harness without using the pink-black wire ?

One wire should go to the battery and one should go to the starter.

There are to ways you can see if your alternator is working properly. The first way is to take your vehicle into your local mechanic and have him perform a load test on your charging system. Most of the time a mechanic will do this for little or no cost because it is easy to do and only takes a minute or so. The second way you could check to see if your alternator is working properly is to disconnect your battery from your car while the car is running. If your alternator is good the car will continue to run until you turn it off. I hope this answers your question.

REPLACE POSITIVE BATTERY CABLE.CHECK ALTERNATOR FUSE AND CHECK ALTERNATOR VOLTAGE REGULATOR WIRES FOR DAMAGE.HOOK VOLT METER TO BATTERY FEED WIRE MAKE SURE 12 VOLTS GETTING TO ALTERNATOR FEED WIRE TO ALTERNATOR POSITIVE HOOK UP IF NOT YOU HAVE BLOWED FUSE TO WIRE FEEDING ALTERNATOR COULD HAVE FAULTY BATTERY POSITIVE CABLE OR CABLES CORRODED NEED CLEANING.

The issue could due to the voltage regulator not working properly.

If the wires have been replaced correctly to the alternator, look for a metallic box near the alternator, probably on the fender wall.

The price for the voltage regulator should be around $20.00.

It is a good idea to replace the voltage regulator when you replace the alternator, since both are probably the same age.

Hope this helps!

If you can give me color of wires you have. My manual is showing about 10 different combinations, depending on whether it has electric choke, idiot light or gauge, ammeter in dash etc. Main wires are Orange, or orange with light blue stripe, goes to FLD on alternator, white with black stripe goes to STA on alternator, and BAT terminal should have a black cable from battery. Be careful, there in case someone changed it to red or another colour , just be sure it's coming from battery, and it may have wire from reulator joined into it.It also shows a ground from regulator to alternator too, so just in case it's black too, don't mix those 2 up.
This may do it, but if not, get back to me.