What terminals are you referring to (where the cables attach to the battery or what?) and what'd you short them with? I can't figure how you shorted the battery or what was involved in the short.
You're getting fuel to the cylinders it sounds like (so the fuel pump is working), you must not be getting spark then or else it should at least try to start. While I don't know enough about what shorted or where or why, you *may* have fried the engine's computer (MPEM... Multi-Purpose Electronic Module) in which case it'll have to be replaced. Ebay is a good source for used SeaDoo MPEM modules from parted out PWC's.
Please provide as many details about the short that occurred as you can remember.
- Michael