I had the exact same problem a couple of months ago on a boat with 22 hours. I changed the fuel/water separator and dumped out almost an inch of water. Installed a new filter and after an hour of running great she stumbled and stalled. Changed the filter again and this time no water was found. I replaced the fuel/water separator anyway. I have put 5 hours on her since without any hesitation what-so-ever. I have no idea how this fixed the problem, but it did. Might me worth another $10 filter.
Good Luck!
_________________
2007 Four Winns 318 Vista "Sas Sea Lady"Previous
2002 Four Winns 268 Vista "Girls Knot Buoys"
1999 Sea Pro 235 WA "Bait Me"