Lets try again… hard to diagnose misfire/hard start issue on an 85T

Many of you know I've been fighting to get my 85T to run properly ever since I bought it 7 years ago. It was so frustrating, I gave up on it for 6 of those years. Well, now I truly need this car to work, so I'm trying again. The issue: Always hard to start after it sits for a while, and stalls and misfires for a while until it gets going. It used to work well after I got it into boost and warmed up a bit, but after I swapped trannys (Auto to manual) now it misfires 24/7, although I believe there are two separate problems at this point.

What I've done to fix it, or try, anyway:

1) Swapped FPR. Both used, neither leak. No change.
2) Cleaned MAF. No change.
3) Replaced CHTS and subharness. Everything improved, but problem persists.
4) Tune up including NGK plugs, new wires, cap and rotor. No change.
5) Swapped trannies from Auto to manual, caused a separate, more severe problem.
6) Swapped ECUs. 85 auto to 84 manual. Idle dropped to the point where it won't stay running.
7) Replaced all vacuum lines except the ones on the turbo, and the breathers. Subtle improvement.
8) New timing belt, water pump, and tensioner. Improved, but same problem present. Timing IS correct.
9) PRW-2 swap. Smoother idle, faster response, problem persists.
10) Deleted fuel pressure solenoid (FPR vac line straight to the manifold) no change.
11) Installed Walbro fuel pump and new fuel filter, no change.

There's more, I'm sure, but I can't remember. As you can tell, I've poured hours and hours into this repair, with very little progress, and now I've even managed to regress a bit.

First and foremost, I need it to run smooth again once warmed up. It always used to, until I converted to a manual transmission. It misfires constantly now, and is generally undrivable.

This HAS to be related to the tranny swap in some way, as it changed as soon as the new tranny went in. Here is what I think could have caused it:

During the install, we broke the exhaust studs on the downpipe (as does everyone else it seems). We did everything we could to remove them, but only managed to remove one. We decided to drill the other two out, but they broke our drill bits! At that point, I gave up, and took it and a spare downpipe I had from an 84T to an exhaust shop to have it repaired. He said the 84T downpipe was in better shape, and replaced the studs in that, and I bolted it up to my '85. It looked identical other than it didn't have a heat shield on top, and bolted up perfectly. The guy who fixed it also said to use copper sealant to re-install it, and so I did. I'm worried this has created some kind of problem now, because it was the only change we made to the engine, other than adjusting the TPS according to the Haynes manual.

Any help would be SO appreciated, I've been chasing my tail for a while on this one, and I'm tired. My daily driver is also dying, and I need the Z to become my primary transportation ASAP. This is all that is holding me up now.