Do you guys have any pictures for reference of the above mention areas to look? As far as the drain plugs go, they better be in - we get out ski's stored, then dropped off ready to go each spring, this would obviously be the best case as it's a matter of putting em in . Will be hard to tell on the lift, maybe I will reverse the ski on the lift to get a better view...Look for a loose hose off the exhaust system. Check especially on the starboard side of the engine where you will see 4 hoses comming out that tie into one line. This area is a common failure point.
The seal around the shaft that p10sdad mentioned is a common failure point on the VX model, but rarer on the FX. Anyhow it is another good place to check. If its leaking there, you have an expensive repair on your hands.
There should not normally be much water in the ski after a ride. The bilge pump should run continuously when the engine is running, and it will continue to run for about 30 seconds after you stop the engine. If you start and stop the ski you should hear it running.
Also be sure your drain plugs are in.
Again, thanks for all the advice!