Is the dealer you are going to the one you bought it from?
I'd find another dealer to work with. I think some dealers just say crap because they know a lot of people have to clue as to what's really going on and they generally get away with it.
How does switching out your flywheels and clutch affect the CSC issue? I haven't read up much on that particular problem.
Read up on the Magnuson-Moss Warranty act, here's an excerpt from the Wikipedia page:
Warrantors cannot require that only branded parts be used with the product in order to retain the warranty.
[7] This is commonly referred to as the "tie-in sales" provisions,
[8] and is frequently mentioned in the context of third-party computer parts, such as memory and hard drives.
I'm not saying that the M-M act will save you or not in this case, I would just recommend becoming familiar with it. The warrantor would have to prove that any OEM parts you replaced with other parts are the cause of the failure...as I understand it. Someone please correct me if I'm wrong.