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Is there an actual shudder w/ clutching action or just a noise?
Was the problem there immediately after parts replacement or how long after did it appear?
Fork and trans input shaft both inspected and Ok also absolutely no leaking oil or gear lube?
What were the face surfaces of FW + PP + Disc both sides also Pilot upon inspection each time apart?
Was the replacement flywheel brand new or resurfaced used?
I didn't see a release brg. on your parts list but expect it's new too?
Don't discount misalignment possibilities and best check detail dimensions also runout of FW and trans input when apart next.
Good luck!

~ Pete
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