Looks like it's time for me to jump in.
- There is a "rattle" type noise, emanating from the bell housing area, when the clutch is engaged (clutch pedal up).
Best to get a video/sound clip of the noise if possible. E-mail to me directly at Sean@weddleindustries.com
[*]Noise goes away when clutch pedal is depressed.
This could mean that the noise would be in the transaxle, but not in every instance. There could still be an issue with the clutch.
[*]The problem seems to get worse as the trans warms up.
This is common as housings expand and tight fitments loosen, and oil starts to thin out allowing for more movement of parts inside.
[*]Clutch components appear to be in good condition with visual inspection.
Verify that the clutch discs are installed correctly. The "snout" of the hubs in the discs should be placed towards the transaxle. It's not uncommon for these to be installed backwards, this is more common than you think.
If you have verified that the clutch is certainly not the problem, then you would need to contact the shop/builder of the trans and speak with them about bringing it back to them for inspection. If there is a faulty part in the transaxle, the builder/shop will work with us to resolve the issue.
For what it's worth, there really are no bearings in the transaxle that will "rattle". They should all have preload on them when assembled. If anything, a bad bearing is going to whine, and will change pitch with engine RPM or wheel speed depending on what shaft it is supporting.
Is this a 5-speed? There have been maybe 2-3 S5 units over the past 10 years that have some sort of mystery rattle (CJ/Mark Hutchins prerunner, and Kevin Price Class 10 car). It would rattle really bad on start up and shut down, but not while driving the car. I spent more time than I care to admit trying to find where that noise came from, but could not replicate it here on the bench. The only thing that we could try and point to was some sort of un-balance somewhere in the engine, clutch, or even a gear in the trans that would vibrate/rattle at those specific frequencies. It's been a few years, but I think after changing complete clutch assemblies and a bunch of parts in the trans, the noise finally went away, but it was never pin-pointed.