I wanted to share this as its the first I've seen this problem on a YJ.
I started getting weird symptoms last winter here in MI where my voltage would spike to 16v! My CE light would come on and the two errors I kept seeing where "charging field circuit short" and also "battery disconected within the last 12 starts".
I learned the voltage regulator is in the ECM. But, my computer is only a few years old. I hoped it wasn't that for sure!
Last week, she finally quit charging completely. Plain and simple alternator failure. Or so it seemed... I pulled the alternator and had it bench tested at the local parts store. It worked perfectly! Darn it... I thought I'd have to go after the ECM. But, the guy at the store said "your connections look like crap, I'd clean those up w/emory paper or sand paper before hooking it all back up". Ok, so I did that. And I redid my grounds.
Heres the kicker... I disconnected the + battery cable when I started taking it apart. When I went to hook it back up, I found my problem. The + battery cable has (2) cables coming into the lead terminal end. One runs down to the starter and the other runs to the power box in front of the battery. The one that ran to the power box was green and cooroded so bad under the insulation that it had actually split the lead open on the bottom side of the positive terminal!
Replaced my battery cables and she's running absolutely amaizing. Over 100 miles now, no slow starts, no sputtering from low voltage, no check engine light and the guage is perfect back at 14v like its supposed to be.
So, Im mentioning this not only to suggest cleaning all the connections, but to suggest pulling off the + battery cable, turning it over and looking for the split w/coorosion on the under side, out of sight.
It was a simple fix, I ran (2) new cables. One to the starter and one to the power box. I attached them to a brass (in place of lead) terminal end w/wing nut. Couldn't be happier w/'er back on the road!!!