Recently my car died on me while driving. All the lights went dim and it finally pooped.

Charged the battery back up and it cranked over fine and then slowly the lights started going dim again.
Well I was driving behind my friend one night and he said my lights were really dim, then a few minutes later got bright again.

The next morning I tested the voltage output on the alternator with my multimeter by the positive terminal on the alt. and the ground on a bolt and it was 10.87 and was slowly dropping to 10.86, 10.85 etc.

So I replaced the alternator, even though when I took it to autozone it tested fine. I'm still having the same issue. I checked all of my grounds, and the wiring to the alternator, checked all of the fuses and everything is as it should be.

So then I thought well the battery is obviously bad, changed it out. No dice. I have no idea why my car won't charge. I've continuity tested every fuse I can find 10 times. I really have no idea what is going on. Is there something in the wiring that could be messed up?

I checked the wire in the 2 pin connector to make sure it was seeing the voltage and it is, so that can't be it.
I'm stumped!
Any ideas?

I'm no magician with wiring issues but it could be a bad ground. It could also be a bad voltage regulator but I can't be sure. Take it to a shop and spend the $30-ish to get the starting/charging system checked out.

You probably have a wiring issue with the small two wire plug that goes to the alternator. One is the field and the other is the charge light. If there is no voltage coming in through the field wire, the alternator won't put out any power.