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I would not rev the engine without the fly wheel if it's external balance.I don't think you can tell if the pilot bushing is in without taking out the trans.How did the engine run when you first got it back together,did you do something afterwards?
If the vibrations come on strong at a certian RPM and then goes away and there is no sign of it before that, then you are hitting a resonant peak in the motor/transmission. This can be caused by anything in the rotating assembly. The normal culprit is the engine to tranny coupling, flywheel/torque converter. If most of the components are the same as they were before the rebuild then I would suspect the engine was not balanced as it should have been. The factory balancing is pretty shabby so a good re-balance should make the engine very smooth. My vote says the engine builder did not do their job.
Did you follow Center Force instructions on the clutch install --I am talking about making sure the bell housing is in a position to insure the imput shaft is correctly lined up behind the crank---Especially if you have already broke an input shaft on the muncie Some bell housings require offset dowels to get it all centered. And all that is still spinning even in neutral.
you have the color I love, mine is mulsanne blue. I also have a vib around 3200, must be 70 blue cars :lol: when I find my problem I will post, watch for it. :cheers: