Two strokes are tough but the snowmachine guys have been doing all kinds of crazy stuff to motors much bigger for quite a while so bombing a 720 should not be too hard and they have to deal with massive altitude changes. You might go over to snowest.com and look in the forums for some ideas. I am sure some of the snowmachine guys could come up with some good ideas.
Some stuff that comes to mind. .
N2O - getting quite common in snowmachines. . Boondocker makes a good setup.
Port and polish. . nothing new here.
New heads. . several guys make custom heads for skidoos, RTK come to mind.
Aftermarket exhaust and muffler. . I have no idea what seadoos run for exhaust or pipes but I am sure someone makes some newer, lighter, louder pipes that give you more bottom end.
A big bore kit to make the engine an 800 or something, I am sure there are guys doing if for seadoos as there are guys doing if for skidoos.
Turbo charge it... ... ... . a few sled guys doing this, I know at least one guy that uses the HY35 from the 2001 automatics on the 800 rotax so it should be possible.
I think you really have to look at what you are going to gain. I have done nothing to my snowmachine because I don't want to hurt the reliability of it but if you did the normal stuff you might gain 15 hp. What does that equate to in terms of speed on the water or overall fun??
Good luck.