Wiring issue, and trans issue.
 

SOOOO, my transmission started acting up, as in not engaging, and my batter light came on.

So, I got a brand new battery and threw that sucker in. Bam! Trans engages and drives like a champ. So, me being the pessimist I am I drove to the local parts store and had them run a batter test, and alternator test. Brand new battery dropped 20% charge from a 1 mile drive. Welp! Need a new alternator.

So, I grab it and slap that puppy in, and heres where stuff gets weird. While in under the car to pull the wires from the alternator i notice that the cable that should continue past the alternator is cut, and well, missing. So, I finish the alternator, start the car, drive it for 3 miles and nothing seems to be wrong. Ac blows cold, battery is charged, and all the lights work. Then I go to pump some tunes and the stereo starts up, but there zero sound.

Wtf, how did the wire get cut and what wire is it? How do I even replace a partial loom?

All I know is that it seems that everything from the positive cable to the alternator is fine. Everything from the first split, at the front of the car, towards the bumper, is fine. Everything at the 3rd split, after the alt, is gone.

Help plz.