Yes I was an idiot for not unplugging the battery before I started doing some work. I crossed the positive cable from the top of the alternator to the alternator casing and heard several loud pops. I fried my alternator so I replaced it (it was putting out 31V after I hooked it back up!). Only the replacement was bad and I drove it to the parts store.
Once I got there my Jeep would not start. I removed the alternator and had them test it and it failed. So I put in a new alternator after testing that it was good. One problem down. Now for the dead battery.
They charged the battery for me and after a few hours we found that the battery was leaking all over the charge station. Bought new battery. This is where it gets interesting...
1. Positive alternator post to frame, engine running - 13.5-14.5V
2. Positive to negative battery post, engine off - 12.5 or 12.8V (can't rem)
3. Ohm test from neg battery terminal to alternator case, engine off - no resistance
4. Ohm test from positive post of alt to the positive post on battery, engine off - no flow (don't know if this is good or not)
MAIN PROBLEM: The voltage warning light turns on after 10 when starting, and the battery is not getting charged. After driving back to the house I tested the voltage between the positive and negative posts with the engine still running and got 11.8V.
What the heck is still wrong???