Austin DeRouchie

Hello, I've been having some troubles after a recent clutch replacement and trans swap. I got the transmission from a junkyard and had it freighted to me a while back and it says it passes tests for function. I'm self taught and this is my first time going about taking a transmission out and when I got everything back together and bolted up(if not to torque spec, atleast tight.. lol) the car started up but has some weird issues. I had it up on jack stands when I first started it and the engine was stuck revving very low and vibrating very bad. You could probably feel it in the ground... You could put your foot to the floor and the engine won't rev up, I was scared to even let off the clutch. It'll run for a few seconds and seem to bog itself out, pretty sure it's pegged at just below idle (like 600). I only ran it twice and after some research I have read of a misaligned flywheel and wondered if this matched any symptoms that people had. I'm going to go about taking the transmission back out on my days off, I've sank a lot of money into this thing. Car has no problem starting it seems, just seems like something is stopping the engine. Any thoughts or suggestions are appreciated for what I should do next.

The car ran fine before I went about the job, My input shaft bearing was failing as when you were idling in neutral you could hear it whirling around in there. Car is also a 2002 6speed manual.