1) The IP voltmeter is a notorious liar. Verify any suspect readings with a "known good" multimeter.
2)
DO NOT do the old "pull the battery cable while the engine is running" test on any vehicle with electronic controls. You stand about an even chance of frying something important!
3) The "on-vehicle" test using the little red Bear ARBST tester that most chain stores have now is reasonably accurate. I wouldn't trust their benches tho - if you've already got the thing off, take it to an alternator/starter shop and have them test it for you. They'll usually throw it on the bench for free, and their bench will not only tell you Pass/Fail, but will usually tell you
why it failed!
4) Sounds like you've got OBD-I. I've got a listing of Jeep OBD-I codes on my site - 12 is "Battery Disconnect" (set when you changed your battery,) and 41 is "Alternator Field Not Switching Properly" - meaning the ECU doesn't see the alternator responding to the regulator output signal. (
http://www.geocities.com/JeepI6Power/obd1.html - all codes listed per FSM.) So, the alternator going stupid on you is a definite possibility, and should be the next thing you test.
A good habit to get into is to, anytime you fix anything that could throw a code on you (you'll see the list if you click the link,) disconnect the battery cables and touch them together for ten seconds
with the engine OFF. This should clear just about all codes, save 12. You may want to invest in a Chrysler OBD-I code reader (they can be had for a reasonable fee - usually less than $100) so you can check things like this yourself, if you don't already have one. You'll note that there are two colours used on the DTC charts I've got up - the ones with the RED background
will light up the CEL/MIL, while the ones with the GREEN background
will not. So, having a scanner so you can just check for codes every few months isn't a bad idea - something could be happening that the ECU isn't telling you about...