How are the main bearings? If they are broken up, and catching occasionally, the flywheel key could shear, but the engine would make noises. The same is true for piston rings catching on a modified port.
1. Is there a loud main bearing rumble?
2. Does it kick back on the starter?
3. Any sign of damage to the flywheel, or damage to the keyway in either part (flywheel or crankshaft)?