When my clutch was slipping during WOT pulls (I didn't know it at the time) but it would accelerate and when you let off real fast you could feel a loud thud/shudder as the clutch grabbed/no longer spun. I assumed my motor mounts were toast. It did this from not long after my protune (30k miles) on my 06 until I upgraded the clutch (86k miles). The 06 and newer models use a similar clutch, but the 06 makes a lot less power stock. Your Stage 1 is where my OTS stage 2 was. The 2.5L has been known to overpower the clutch at stage 2 levels.
FWIW mine no longer does it since I upgraded the clutch.