Hi,
I also own a 98 gtx limited and had a similar problem. The problem I had was that carbrator wasn't ajusted right and was fowling out my plugs. On the top of the carberator you can ajust the carberator by truning the low speed needles. There should be two, one for each pistol. What this does is allows more or less fuel into the carberator. My guess is that these needles are allowing to much fuel into the engine, which would cause it to cut out. If you pull the plugs and find that they are "wet" and smeel like fuel this could be the problem.
If you do adjust the needles you only need to turn them about a 1/8 turn at a time and then try running the ski again. After you adjust the low speed needles you may have to ajust the idle needle also. The enigne may idle to fast. Out of the water the engine should idle at about 3500 rpm. Just as a reference I had to adjust the needles on my ski to be about 2-1/4 turns from fully closed.
One last thing is that when you run the engine out of the water you should have the hose hooked up to the ski or else the engine will overheat. (I asume you already knmow this, but wanted to make sure.)
Hope this helps.