Will the dealer replace the stock clutch under warranty?

It will only be replaced if it has a factory defect and if it has less than 12k miles. When I say defect, I don't mean the clutch starts slipping. I mean a spring fell off the disk and cause the entire thing to fail or the throwout bearing failed. This is extremely rare, though, and they first have to take everything apart to see if it's a defective part that is covered under warranty or simple wear and tear (or abuse), which would not be covered under warranty.

I blew out my stocker at 7500 miles after lots of drag racing and autocrossing (many 12.2s and 12.3s in the 1/4). when they took it apart, both the pressure plate and flywheel were turned into mirrors from excessive heat, so it was obvious that it would not be covered. I just had to pay to have the ACT installed and go on my merry way.

That's wholly dependent upon the dealership itself. I went to the ONLY ONE of seven local Mitsu dealers that any of us trust with aftermarket stuff. They not only have a Master Tech who is intimately knowledgeable of DSMs and Evos from a Mitsu perspective, but he also does his own work on the side. They installed everything for me and said that the presence of the clutch would not void any future/potential drivetrain problems other than the clutch itself, especially since they know they installed it. Even so, they said they wouldn't deny warranty claims on the drivetrain even with clutches installed by someone else unless it was obvious that the clutch itself caused the damage. You won't find that everywhere...