Hopefully you have a service manual, as it has detailed proceedure & pics, ect. You will need to remove the jetpump. Align the engine when
you re-install your engine. Likely the driveshaft will come out when you pull the pump back from the transom.
You can put a vise-wrench on the driveshaft and tap it back if the d-shaft sticks in the PTO. Roll it on a flat surface to determine if the shaft is straight or not. The '96XP service manual is a GOOD FRIEND!
http://partsfinder.onlinemicrofiche.com/seadooforums/Seadoo_oem/Seadoo_PWC.asp?Type=12&A=35
INSIDE: remove the clamp on DS at PTO. Remove large supply hose & two small syphon hoses from JP thru-hull tubes.
disconnect the carbone ring by pushing foerward with thumbs on ring to reveal ring clip and remove that.
OUTSIDE: remove steering bolt from steering nozzel, remove the four nuts-lock rings-flat washers from transom studs.
gently wriggle pump with a bar to loosn pump and pull off. These sometimes are hard to get because of the silicome
at the pumps tru-hull tubes (prevents water intrusion). If thats the case, use a pump puller as detailed in shop service manual.