2000 Pro air GT 40 not running

2 months ago, I uncovered my boat and fired it up for the first time this year. It ran for 30 sec then sputtered and cut off. After a lot of checking, I put a vacuum gauge on the fuel pressure regulator and the boat started running. I figured that the diaphragm must have been stuck. It ran rough for a couple min when I first took it out but it cleared up and has been fine ever since.
This weekend, I tried to take it out and the battery was dead. I jumped it off and it ran for about 30 sec and sputtered and cut off. It would not run at all after that, just turn over. I tried playing with the regulator again and that didn't work. I tested the fuel pressure, and it was at the recommended 39 psi and it dropped to 32 when I put vacuum on the regulator (which I think is correct operation). It has spark, the fuel looks good (no water), and I replaced the fuel filter 2 months ago. I can hear the priming pump running also when I push the start button. I'm kind of stuck now. Any suggestions on where to look now? Thanks in advance.

Its fuel injected. Its a 2000 with a power boss GT 40 351

I have gone through some of the threads and got some ideas on a few things to try. Thanks for the link

If you put it back together again and have troubles. Check anti siphon valve for a sticky ball, blocked tank vent,and screen on gas pickup clogged.

Stabil marine formula. I also tried a can of SeaFoam to try to clear it up after I found the problem but that didn't work.

thecoxshow wrote: Stabil marine formula. I also tried a can of SeaFoam to try to clear it up after I found the problem but that didn't work.

There isn't a product made that will completely stop phase seperation or reverse it.

I agree, when I put it up for the winter this year, I'm going to leave it empty and just dump fresh gas in it next year. I realize that condensation could be an issue, but I'm going to take the risk.