Alright, I probably should have updated a while ago, but I barely have enough time to check on TR these days.
Anyway, the problem was the Turbo itself. It was blown to bits. So much so that the propeller and compressor fans were scratching up against the housings at an incredibly aggressive angle. That's why there was so much resistance past 3.5k RPMS.
It would also spit out oil all throughout the intercooler piping and the Intake manifold, due to the blown seals. The turbo was literally kicking it's own ass. Well, I have a few CT26s lying around, but they're all blown, and I've never rebuilt a turbo before. And although I'd love to give it a try and rebuild one someday, I wouldn't trust my amateur build on my Supra. I had no choice but to buy a new one. And I figure since I'm going to buy a Turbo, I might as well upgrade. I didn't want crazy power since, this was going into a DD Supra with way too many miles to even consider performance. So, I bought a freshly built 60-1 CT-26. During the removal and install, I stripped every bolt, and nut you could imagine, and it ended up taking me two days just to remove the turbo. Puddles of PB Blaster sitting on the nuts overnight helped me out. Anyway, once the turbo was out, and the coolant was drained as well as the lower coolant hose removed, I took the time to inspect as many vacuum lines as I could see. I found about five completely severed lines, and I replaced them. Hoping for the best, I installed the fresh turbo, and started putting everything back together.
Once the turbo was finally in, I filled the radiator with coolant, and I tried to burp the system, but it wasn't really working, and the Supra almost overheated a few times.
Eventually, I got it all settled. and I took the Supra out for a spin, at 3am (when I finally finished). I finally felt my Supra boost for the first time ever. It felt awesome. Conclusion? The car was unable to rev past 3.5k rpms because the turbo was blown, and there was just too much resistance from the turbo that it was overworking the motor. The car would stall out constantly because of all the damaged vacuum lines.