Overvoltage and a broken alternator harness

My jeep had a low voltage warning driving the other day. I pulled the battery terminal when it was running and it killed the engine. When I tried to start it later on, it was totally dead. So I assumed it was an alternator problem and replaced it. I charged the battery and started to drive home, but didn't make it. So I got it towed and started to look closer at it and found a broken wire on the alternator harness right at the black molded plastic box. It was broken such that I couldn't splice the wires back together. So I made a jumper with a ring terminal. I wasn't sure which wire went to which post on the alternator, so I tried one. When I jump started it and disconnected the jumpers, it died slowly as the volt meter dropped off. So I swapped it to the other post on the alternator and it ran mint. Volt meter was right in the middle where it always is. So I started driving it and it overheated (a different issue altogether). Got that straightened and went to drive it again annnnd over-voltage. The meter was pinned at 19V. Shortly thereafter, the engine died and now there isn't a hint of electricity anywhere in the vehicle. No clicking with the key, no lights, no beeps. And the volt meter is still pinned at 19V.

What happened and how do I fix it?

Hey there Rob,
Are you sure that the battery is ok?
There is a fuse able link where the alt and battery wire meet,,, the terminal at the end of the under hood fuse box.
at the same terminal where the pos batt cable connects to the fuse box..
..

The battery is pretty new (~6 months) but that doesn't necessarily mean it's good. But let's assume it is for now. There are two major wires coming off the alternator, which one meets the battery? And it meets the battery positive or negative at the fused link?

I poked around a bit last night and made sure that I had good connections. I cut both small wires from the black plastic box and made jumpers for each. I made sure that they were connected as original (same wire to the same post). I started it and let it idle to warm up, keeping a close eye on the volt meter. It was going fine, everything seemed normal, for about 5-10 mins. Then the volt meter spiked to 19V and I shut it off and gave up. I don't get it.

Second hand info,,
Assuming the alternator you recently installed is a properly working alternator:

check the voltage at the back of the alternator vs. the voltage at the battery. If the alternator is reading 18.5V, but the battery is reading substantially lower, you have a resistance issue, and should have the cables load tested.

If both readings are high, have the battery tested first. If the battery tests fine, I would look into changing the ECM.
Did you ever get you wipers working properly ?
I'm assuming that you can't drive it over here, If you want to trouble shoot yours and need a comparison vehicle, mine and Carol's jeep's will be here over the weekend, both are 97's

Thanks Mark. I'll check those things when I can. The wipers and turn signals still work all the time (unless the battery is dead   ) I dunno what's up with that, but I can deal with it if I can get the Jeep running normal again. After the voltage spikes, how long is it safe to run it (assuming it'll stay running?)? I mean, are we talking on the order of seconds? minutes? I shut it off immediately last night when the voltage spiked. The time before, I was driving, and everything seemed normal for about a minute, then it just stalled out. I think I'll do the voltage tests with the old battery just in case, get the results, then install the new one and see if there's any change.

I'm not sure about driving it,, I had a low voltage/check gauges light come and the dash gauges shut off. This happened a few separate times when I was winching with it running.
After a few miles of driving It I stopped, shut it off and started it up again and all was ok .

If you had the battery disconnected and you attempt to connect it does it have a heavy arc/spark, assuming that everything in jeep is shut off what does it do?

Put a volt meter across the battery terminals with the cables disconnected and note the voltage, then do it while the cables are connected.
Survey Says ?

No offense to you Mark, but I said to heck with your tests. The girl was over, so I didn't want to spend any more time than I had to under the hood. I sent up a prayer and just put the new battery in. Problem solved. My best guess as to what happened is the following:

The alternator wire broke (the small green/red stripe one), probably just due to old age and becoming brittle.
Unaware, I continued to drive, just on the battery.
The battery died, and the symptoms at the time were consistent with a failed alternator (disconnect battery cable while it's running and it stalls).
I replaced the alternator and charged the battery (I was at work, and it was down the street, so this was easier than getting a jump).
I drove home on whatever charge was in the battery, but didn't make it very far.
So at this point is when I began to see really odd symptoms and I think it was because the battery was ruined by running it down to nothing twice. I think that the battery being dead (not just un-charged, but unable to hold a charge) caused the charge circuit to go haywire. It would begin to charge the battery normally, but then when the battery discontinued to accept incoming charge, the PCM told the alternator to increase the voltage to the battery, hence the spike I'd see on the gauge. Then I'm not exactly sure what would cause the whole system to shut down. Probably because the alternator was getting overworked and underpaid? I only witnessed this shutdown once. The rest of the times, I'd shut it off with the key so as not to ruin anything else.

That's my best guess based on my rudimentary understanding of the charging system in these things.

So, long story short, the new battery accepts the charge as normal and I fixed up both small wires to the alternator (skipping over the plastic block) and hopefully it shouldn't occur again. Thanks for the help as usual.

Well it's great to hear that you got it fixed..
I believe that you said that the battery was 6 months old or so but obviously they can go bad, for whatever reason.
If you checked it,, What did the old battery read for voltage not connected? just curious,

I checked it while it was connected, but the engine was not running and it was 12.xV.