The rear diff was leaking out of the right side, and for some reason the axle from the manual appeared to be longer on the right side. Long story short, I ruined the corroded diff trying to change the seals. Got a new (used) diff and eventually replaced the right axle with one I had lying around from the junkyard. So far no more diff leaks. I've put more than 9,000 miles on it so far.
I also figured out the abs. I tried plugging in the TCM and It idled high (2k rpm) but the abs worked (light off). So I randomly realized I could try plugging in one of the two plugs on the TCM. Tried one and the abs still didn't work(light on) and it idled high still. Tried the other plug and the abs works! And it doesn't idle high. Problem solved.
Also, we found the pin to tell the car it's a manual. Now I only have 2 CELs, o2 sensor (unrelated to swap) and starter circuit low voltage. But I have another annoying problem. When I let off the throttle (when I'm changing gears for example) it holds the throttle for a second or two after I let off, and I'll have to wait to engage the next gear. It's really annoying. If anybody has any input it would be appreciated...Still haven't wired up the NSS. Could be an issue with that, or it could be the intake, just don't know exactly what needs to be replaced. Will post if I figure anything out.