hmmm, that sounds really odd. When you say "its when i put my foot down a bit for the first few seconds", is that with clutch fully released?
The clutch is seperate from the clutch hydraulics. There will be a bleed nipple on the slave cylinder bolted onto the bell housing. Bleed in the same way you would the brakes. Having said that, the way you describe the symptoms, it doesn't sound like the hydraulics anymore, but I would still double check it just in case fluid contamination is an issue. If there is a leak, your clutch fluid level will be low, so a pretty easy check. It almost sounds like your engine mounts are shot or something. Maybe the removal of the gearbox to do the clutch settled the mounts but they have now come loose again. Sounds odd. If the clutch isn't slipping, then I can't see the flywheel being the cause of the noise, but I guess anything is possible. If it was doing it before, and then started after, I would expect the clutch people to spot any flywheel damage, but then again, they should've spotted fluid leakage too if it was happening.