Be very careful jumping these skis. Yamaha does not recommend it....you can fry the electrical system. Best to jump from a pulled battery, or even better just connect to a known good battery.
The owners manual is a free download. Get it here:
My Yamaha Prompt - Owners Manual
Check the fuse (location in the owners manual) you may have blown it with the jump. The manual shows the recommended way to jump the ski. Check for loose connections at the battery and the electrical box. Go to the section in the manual about resetting the PADLOCK system and carefully follow the instructions (be sure you have a known good battery connected when you reset the system), then try again NOT with a jumper system. You should hold down the mode button, and the system will ask for your code, then you should see START.