You might want to look into a 'Megasquirt' or some of the other aftermarket ecm's that are availible, they are being used on everything imaginable. There is at least one guy that I know of on the Megasquirt forum that's using one on a Sea-Doo and it was installed on an originally non-computer controlled ski I believe.
I can't say for sure it would work on your particular ski, but I can't see why not, it already has all the sensors and pick-ups for the required computer inputs because it's already computer controlled.
Something to consider anyway . . . . . . .
'Crockett