Steve, what are you using for an exhaust manifold.  I ask because on the
Porsche engine, with the short exhaust pipe length and the exhaust manifolds
I originally used, there was an amazingly loud resonance in the exhaust
system at about the rpms you are having your problem.  Truly sounded like
something large and loose banging against something else metal.

Now I have the earlier manifolds, with longer distance from exhaust port
to the place where the pipes 3->1, and the relatively enormous stock
Porsche muffler, and the problem is completely gone.

Not an explanation for broken clutch disks, but something to consider 
relative to your vibration.

Glad to hear you have all six back on the highway in any case.
B.
Wm Kennedy
kennedy@admin.njit.edu