Did you find the internal carb fuel filter? If not here is a diagram to help you. It's part number 7 on there. Looking down at the carb there is a cover with four screws. Unscrew those, take the cover off, and there is a black plug like thing in there that is the filter. Remove it with needle nose pliers if you can't with your fingers. If its dirty use some carb cleaner spray to spray it out.
http://www.mikuni.com/pdf/sbn_rebuild-kit.pdf
Is your compression good? The 2000 GTI has the 717 aka 720 motor which should have 145-150 PSI of compression.
If all this pans out you probably need a carb rebuild kit. Your watercraft has a Mikuni BN 40-
38 carb.