I did get the alt tested just to rule it out and it tested fine. I installed it back in the jeep and it was showing low 13 volts on my meter at idle, then it went down to high 12s after I turned on the headlights.
I'm beginning to wonder if my ground is not adequate. I cleaned up all the grounds I could find except the big negative battery cable. Its attached below the AC compressor IIRC and was difficult to access so I left it alone since it seemed fine. But I had a weird experience with jumping the jeep with my wifes van that confused me.
This didn't make any sense to me, but I hooked jumper cables to my wifes van and to the jeep battery terminals. My meter on the jumper cable clamps on my wifes van's battery read 13.6v. If the cables were unhooked from the jeep then the other end of the cables would read the same as expected. However once I hooked them up to the Jeep terminals, the cables would read 12.6 again.
I could literally remove the negative cable, put it somewhere else on the body (or remove them completely) and it would show 13.6 (same as the van), but whenever I put it straight to the battery it would go to 12.6. It doesn't make sense...the jumper cable is just a large wire and it should read the same. So I'm wondering if my engine to chassis ground is not good enough. After messing with it I finally got it to show right around 13V and the Jeep started up great. I let it run for about 15 minutes before shutting it off to see if it had charged the battery and the Jeep fired right up again. Again, I know bad grounds can do funny things but I have never encountered this issue with any old car I've resurrected.
I have two meters; one from HF and a Fluke. However, the Fluke doesn't show me the decimal points of the reading so it will only show 13v or 12v whereas the one from HF will show 13.46 or 12.68 for example. My HF meter is older and the probes are bent/worn out so I want to get a fresh meter and see what it's saying.