The fuel pump is part of the first carb, the one nearest the front of the engine referred to as the mag carb. There is also a small filter in each of the carbs. Taking off the carbs and opening them up to get at the small filters is a delicate operation, but can be done. I found that the inlet elbow into the first carb was all but filled with the blue green gunk, the filters were dirty but not completely plugged.
I decided , since I was on a roll, to replace the fuel lines and clean the filters on my wifes 96 gtx. I knew I was breaking the rule, "if it ain't broke, don't fix it". I found that even though her ski ran very well, it had a lot more of the green gunk and dirt than I found in mine. After I got it back together and on the water, it wouldn't run well at all. As soon as I tried to open it up, it would die. My buddy suggested switching over to reserve, I thaught he was nuts but did so, it ran much better, wouldn't go over 35mph though. I bypassed the reserve valve, and the ski ran like new. I think the ski was sucking air at the reserve valve. I would suggest, removining the shortline from the fuel filter leading to the reserve valve. Remove the reserve line from the fuel baffel (pickup) and connect it directly to the fuel filter. Check the "O" ring on the fuel filter. Check all of your connections, there are a lot of places that air can be drawn into the system rather than gas. There are also two vent valves in the system, one goes up from the "t" that lets air in, the other goes out through the hull, just under the gunwale that lets excess gas pressure out of the tank these can get clogged.
If none of the above works you might need to rebuild the carbs, check out
Complete Sea Doo Single & Dual Carb Rebuild Packages - OEM Mikuni Parts for info and supplies.
good luck......