For bias reasons I'll obviously say get an M3 but if that doesn't float your boat, I wouldn't hesitate on the C63. The trans isn't that much of a slouch. Granted its not on par with DCT and since you're not tracking the car, I'd get the AMG based on your quest for torque. You won't be disappointed.
Edit: I just re-read your post. When you said the only thing you are second guessing is the auto trans, did you mean how it shifts or you were referring to the sheer lack of an option of a manual trans in the C63?