Okay, I got the car back together and running. Dropped it off at a muffler shop today to have them sort out some new mounts.
I found that a PO had installed a wideband o2 sensor....but didn't actually wire it to anything. Since the original wiring was still in there, I put in an OEM sensor and will hold onto the wideband in case I upgrade the ECU and stuff in the future. The car seems to run much better with the o2 sensor actually sending some data.
Had to replace the alternator, it has an internal regulator so I thought I could take out the old reg that under the panel on the passenger side. For some reason I couldn't get it to charge so I tried connecting those wires again and it seems to be charging correctly...but I thought this would mean two regulators in the system which is bad? I thought the reg was a leftover bit from the pre-280zx motor swap but its still a struggle to figure out what bits of the wiring system are from the old vs new setup.
Also, now when I hit the throttle and then release it, the idle drops super low and sometimes recovers, other times it dies. If it doesn't die it will come back up to a good idle. I don't know if this is effected by the TPS setting, AFM settings or something about the edited vac system. I am still try to research this area but I am also planning to drive it to a local mechanic who specializes in z cars for advice.