I went down this road also Chad when I first put my GM crate motor ZZ454 in years ago. Same exact vibration problem, except I had an automatic. Did nearly all the same things you're doing. Compression check, fuel pressure check, spark plug and wires check(and distributor), harmonic balancer check, mounts check. I eliminated some vibration when I found a bad spark plug wire arc'ing over to my block causing a misfire. But still had some vibration so I then detached the torque converter from the flywheel and shimmed the transmission back to allow the engine to run while detached from converter. I noticed very little vibration then. So, to make a long story shorter, most of the issue was with my flywheel and how the converter was bolting to it, and a new flywheel solved that. I still had a slight harmonic vibration between 1500 and 3000pm after all that, but it was basically just a result of a big cube motor and I came to that conclusion when I sat in somebody else's ride who had the same ZZ454 and it felt exactly the same at the steering wheel.
It drove me nuts for quite a while so I hope you get it sorted out soon and it's something simple.
