The front of the intake plenum, and spark arrestor are both seriously rubbing on the fiberglass drip rail. That issue alone would cause even a smooth running engine to
sound like it is vibrating. I would suggest fixing that first before taking anything apart!

Good spot!

I would agree with you if that piece were in place the way it should be. In the photograph it is literally laying on the engine before I got it mocked up in its proper location I have a good inch between it and the intake/filter.

I always thought flywheel holes were drilled such that it would only go on one way and all the holes line up. Found out that is not the case, and it definitely caused a vibration.

With Merctrans...assuming the block is a Mark IV 2 pcs rear main crank with the MPI added to the 9lder block?

Or one pc rear main crank Gen V or VI?

This seems.to be an issue from the the 1st time you saw it, and never.seen it smooth past 3000 rpm?

Maybe it has an internal balanced flywheel on it.