Re: 96 GSX Seadoo problems!
the filter is BEFORE most of the fuel line, and besides, most of the stuff from dissolving lines will pass through a sediment filter. (GSX's don't really have true paper element fuel filters, the filter they have is just to trap the larger particles via a small mesh screen)
If you have grey fuel lines, i'd be willing to be your carbs are plugged up. Those lines WILL dissolve over time, especially if you have ethanol fuel. If they are the grey colored lines, don't run it any more until you get the carbs cleaned out and new fuel lines. Later models got black fuel line, I think most '98's had black.