I may be way off on this one, but it sounds like the pilot shaft might have galled roller bearings internally.
I have to wonder why, with a new engine you went gear drive. I have had them and I do not like them at all. Just my feeling.
My other thought might be a loose flywheel at the hub. However, when I had one, it had more of a feel through the pedal rather than audible.
After all that work, that must be very frustrating. I just spent two days diagnosing a missplaced spark plug wire. After all the engines I have built, cars I have restored, rods I have built, I had two plugs off on the cap. It is a big block, and I have not had a big block for years.
Like Duh!!!!
I hope your fix is that simple.