engine stalls

I have a 99' Pro Air Nautique with the 5.8 HO PCM GT 40 engine. The last 2 seasons I have had a problem with the engine almost shutting down then coming back when operating at skiing speeds. It never completely stalls. Never does it at idle. Is totally unpredictable. I took it to the shop end of last season and they said it needed a new fuel filter. Seemed to be better for the first few hours this year then came back again. I replaced the low pressure fuel pump, no difference. Only got out 5 or 6 days this year, but each time it is becoming more frequent, but not often enough that I think it will do it for the mechanic unless he runs it for a couple hours. Very frustrated! Anyone else have this issue or ideas?

Here is the troubleshooting thread:
http://www.correctcraftfan.com/forum/forum_posts.asp?TID=25584&title=poor-mans-gt40-diagnosis

The thread Gary linked too ends with the problem/fix being the tube inside the Fuel Control Cell. That's definitely one of the first things you want to check.

i had similiar symptoms. it turned out to be the EEC relay, a $15 fix. I would check the line in the FCC , and change out both relays. My boat did not stall at first, but the boat would "shut down" for a 1/2 second and pick right back up. I let it go for a couple of weeks and the boat began to stall. It would start only after a couple of failed attempts. The fuel pumps were not priming. Other than the "miss" and the stalling the boat ran excellent.

       

Yeah, my idea for the thread was to try and keep it simple.
Did you see the Spreadsheet?

Keep posting what you try and find, and people will weigh in. Be sure to post your results as well.