Well, I've found something new that might be an issue. I have too much delta at the u-joints. It's 5* at the front u-joint and a little over 4* at the rear u-joint. The transmission is lower than the rear end so I'm going to raise it with shims to see if that will flatten out the angles at the u-joints. Might need to pull a shim out of the rear end too but that's no big deal either.
I don't see how this could be the issue necessarily though. Before I did the suspension work, the rear sat lower than it does now due to the worn out factory springs. That would have made the angles worse. Yet, I had no vibrations then.
[light bulb!]
As I'm typing this I just remembered the front end used to sit higher too though. I've brought the front end down with the coil overs compared to worn out factory coil springs. That could be the reason I didn't have the issue when I first did the engine and transmission swap. Yep, going to raise the tail of the transmission.
Oh, and I have 1-1/2 inches of yoke shaft sticking out of the transmission currently. I still have plenty of engagement with the tail shaft. Could this be too much though?
Thanks