Hi,
If you had the flywheel properly surfaced (not with a hand grinder like some shops) on surfacing machine and new disc, and you have no oil leaking from engine or tranny in to clutch that should eliminate that. ( If a hand tool was used you probably have a very uneven surface)
you mentioned thumping in front, how about checking for a loose or broken engine mount? Open the hood and have a helper watch the engine as you carefully try to engage clutch with car blocked or e-brake on if the engine tends to rock way up this could be the trouble. also physically inspect it and check by a bar trying to lift engine.
You also mentioned the pilot bushing wore funny, then how is the tranny input shaft bearing?
another thought because you say you have to run with the choke out some times, have you checked for vacuum leaks which can cause the engine to rough on take off? also is ignition timing properly set for that cam?
Just a few ideas for you, Scott T.
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