Hopefully i can help..
You say clutch pedal is pump? On its own or when/during depressing its felt?
Does this thumping noise coincide with the pedal pumping/pulsing?
Does it get worse as you rev up or thumping even out?
What other checks where made bar just the flywheel/clutch change?
Hi..there sorry for the delay..
Ok..I couldnt see it being the injectors causing this problem especially as far the clutch pedal goes,injectors would usually cause running issues/missfiring general performance issues as far as the engine goes..the problem going by your description would relate to most likely missalignment or something with slight run out causing that thumping/pulse sensation to travel up the pedal a bit like a warped brake disc if thats what it feels like..obviously of course things like transmisson/engine mounts would be something to include during checks..seeing as the i asume the whole assembly clutch has been changed including flywheel as long as that beeen fitted correctly,everything seated properly.it possible it could be bottom end trouble.maybe slight run out on the crank flange could cause that that the flywheel mounts to..only way to tell would be to run a dial guage to see if that the case obviously this would mean strip down again to check that
No crank has to be replaced..the flange is cast to the crank which the flywheel is bolted too..Thats why it would be worth at least checking the mountings first carefully..