Well I do not know where it is coming from. The car has always had a vibration from 3400-4000RPM but that stopped after the tranny and transfer case was replaced. I posted it on here a while ago and some thought it might be the balance shaft was out of phase or not working at all. That is most of the reason I bought and gave you all the components for T-belt and balance belt replacement.
My suggestion would be to have one of the guys (JET maybe) drive it to feel it also and maybe track down the source.
You say it is in the frame...then windshield? Is it just an engine vibration maybe from a bad motor or tranny mount? I did not replace them at anytime nor did the previous owner as far as I know.
I did not feel a vibration the entire drive out nor when you were beating it...I mean test driving it before you paid me for it. Maybe you tore something up in the tranny with that missed shift/slam when you were test driving?
Hope you get it sorted out...Kenny