I had a similar issue a few weeks ago, but my boat would run fine only in low rpms's.
Ended up checking the fuel lines and they were completely shredded on the inside from sitting with bad ethanol fuel in them. I swapped my filter, cleaned out my fuel pump, replaced the lines and everything is golden.
Probably not your issue, but just thought I would throw it out there. If you search you can find pics of my whole experience on here...
Good luck man!