Sorry I let this go guys, I got really busy with work. I'll try to give you all the info this time. I'm going to recap a lot, but also provide new / hopefully helpful info:
Body of the car is an '86 DL sedan w/ d/r 5spd.
EJ22-t and harness is from a '93 legacy wagon.
The alt on the car currently has been tested good by a local battery/alt/starter shop.
Voltage between batt to block, block to body, body to batt are 0.00V.
Alt wiring:
The three wires from the EJ alt pigtail are fat white, yellow, and black/white.
1. The fat white goes into the stock EA fusible link box. There are three fusible links in here, but I'm not sure where they all go. On one side of all three fusible links is the battery. On the other side of the fusible links are three wires, A) Fat white from alt, black/white, I don't know where it goes, C) white/black, I don't know where it goes. I can attach a pic of the fusible link box if needed, but like I said, it's the stock fusible link box in the engine bay, so I'm sure you've seen it before.
2. Yellow wire from the alt goes to switched +12v.
3. Black/white wire goes to an after market voltmeter.
Symptoms: Voltmeter jumps around, anywhere between 11-14.5 volts while driving. Both the stock voltmeter and my after market voltmeter does this. It seems like if I accelerate quickly (like get on the freeway) it's even worse (fluctuates really fast).
The battery is never dead, but I notice when I turn the key to on, more often than not, I have 11 volts or less. Also, my radio seems to lose power when the voltage fluctuates towards the lower side. I'm not sure if this is all related, but I thought I'd list everything. When the car is off, the battery reads 11.6-11.7 volts. This is a brand new Optima red top battery.
Also, I can hear my fuel pump slow down when the volts drop.
Thanks again all,
-Jason