Did you use a dial indicator to see if there is any runout on the bottom of the crankshaft?
It would be more accurate.Or use a coathanger afixed to the fame and rotate the engine by hand while someone watches to see of you have the slightest of run out.
Also, its a shot in the dark, But I have seen that exact issue caused by loose engine bolts or a cracked mounting plate where the engine bolts attatch to the frame (On One. the cracks were under the block so you souldnt see them unless you lifted the engine block. That one was on a garden tractor with an overised engine that was retrofitted on it. Exact same symptoms as you desribe. You should be able to see from underneath, but not always.That one took me awhile to figure out as it looked fine from underneath. It wasnt a horrific vibration, just really annoying.