I have a similar problem with my 84 H.O. Didn't notice any vibration (only got to yard drive it first) before pulling the motor to put in the 63 Falcon.
I bought a new RAM clutch kit. I pulled the alignment pins to get the flywheel resurfaced, but couldn't remember where I put them.
Anyway, when the clutch (10") I ordered came, there where no alignment holes for the pins and the bolts had shoulders that were tight fitting through the mounting holes.
Part of the vibration I had was the exhaust up against the trans mount. I fixed that but it still seems to have more vibration than I think it should.
I also used new Bronco motor mounts to get the extra hight for header clearance. Could these mounts be too hard causing extra engine vibration?
Or does the weight of the three pins have anything to do with the balance as well as alignment?

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Dan

63 Futura
59 F100
40 Ford PU
39 Ford PU