The jet pump will have a rattle noise when running on the hose, but you won't hear it in the water as water pressure adds a load on the jet pump so it goes away. Look in the jet pump to see if anything is up inside the jet pump area. If not, next remove the spark plugs from the engine and connect the plug caps on the grounding studs. Then hit the starter and listen for any noises. The clicking might be a bearing in the jet pump that needs service. You could also remove the nose cone of the jet pump to see if the oil is contaminiated and change it. Here is some info if you do that;
If you look into the nozzle in the rear of the ski you will see a cone with 3 screws and an oil filler allen screw.
To change it,
1) Take off 4 13 MM bolts holding nozzle and 10 MM bolt holding steering.
2) Get something to catch the old oil in, drain pan or margarine cup etc.... (don’t forget the nose plugs, the oil stinks to high heaven)
3) Remove the 3 8 mm bolts holding the cone on.
4) Pull the cone and drain the oil out. Prop the front of the trailer up as high as you can to get most of it out.
5) Inspect the rubber “o” ring and if it is good apply silicon and reinstall the cone. Make sure the allen fill plug is on top.
6) Lower the front of the ski and add oil** to the cone. When it is full, take a brake and have a drink. There is air in the cone and when you go back you will see that it is low. Top it off and take another brake... do this until the fluid does not lower again. I often start the ski for a few seconds to make sure oil is all the way worked into the bearings and all the air is out.
7) Wipe silicon on the set screw and screw it in (be sure not to run it all the way into the cone. just deeper than flush is fine. Let it sit 24 hours to cure the silicon and put the nozzle back on.
**NOTE: Use Sea Doo 75w90 GL5 Synthetic Polyolester Oil
I hope this helps.
Karl