Were not getting any fuel in the fuel filter
Did you add your own inline fuel filter, or do you mean the fuel/water separator that looks like this:
http://www.2040-parts.com/_content/items/images/81/833981/001.jpg
It's generally not recommended to add an inline fuel filter. There are multiple fuel filters already and they generally work well.
If the fuel/water separator is not filling with Fuel, then:
1) Your fuel pump isn't functioning OR
2) There's a block/leak in one of your fuel lines OR
3) The fuel selector isn't working right OR
4) The fuel tank is empty
Verify you have fuel in the tank (did your gas gauge fail?). Verify the fuel selector is set to either reserve or ON. Try holding the choke and holding the start button for 3-5 seconds. The fuel separator should now have fuel in it. If not, let's talk about how the fuel pump works.
The fuel pump has two one way valves and is inside the forward carbureator (if you have two carbs). It looks like this:
https://i.ebayimg.com/images/g/258AAOSwCypWppYc/s-l300.jpg
There is a diaphragm on top of that assembly that flexes in and out from a pulse line from the engine. As it flexes, it pushes air/gas through the two one way valves and pumps fuel. It actually pumps quite fast--even after replacing all fuel lines and emptying the water separator in my '96 GTS, it filled the entire system in about 3 seconds of cranking.
If the fuel pump has failed, it could be because of a leak in the diaphragm, disconnected fuel or pulse line, or some other failure. Check that the pulse line (the short fuel line that goes from the engine to the carb) is connected and not leaking.
If there's an internal failure in the fuel pump, a carb rebuild will fix it. There's good information on how to rebuild your carbs here:
The Seadoo Carb Rebuild Thread
Don't try to take the carb apart and just clean it. If you get your carb apart, clean it *AND* rebuild it as described in the thread above.
Have you replaced the fuel lines? The original fuel lines are grey, and are known to disintegrate into a green goo which gums up everything and blocks fuel flow. They should be replaced with modern automotive carbureator fuel lines. If you haven't replaced the fuel lines, you need to replace all of the fuel lines *and* the fuel selector *and* rebuild the carbs. If this hasn't happened, this is the first thing you need to do when troubleshooting.
I replaced the fuel lines and rebuilt my single carb, and it took a little more than a day. I'm quite slow and not much of a mechanic. But my 1996 GTS now runs like it's brand new. It starts easily and it runs great at all speed ranges. It doesn't hesitate or cut out--all behaviors that I was told: "the carb models just do that". Well, if they're maintained properly, they don't...
Hope this helps.
