Well if you use a 550, you won't be able to get your Factory pipe in there without a redesign of the hood. I cut off 1" on my 750 and 3" on my SJ. I wouldn't go any further than that. -1" on a 750 is fairly tough to handle and I only weigh like 165lbs wet...
If I were to chop another inch off the 750, a flatwater backflip is out of the question because I would make a tight turn to get back to the setup wake and the wake would be gone by the time I got the ski moving forward again. Believe me, it takes some careful throttle feathering for me to get the 750 moving forward after a tight turn or big jump.