I have had this problem reoccurring for a few months now. I purchased my 2002 Elite V with a known intermittent bogging issue. I determined it was isolated to a fuel pressure issue by running a mechanical gauge on the fuel rail. What happens is when I am going 3/4+ throttle, the engine will completely bog to idle rpm, then shoot back up, then bog back down. This problem is intermittent, and really noticeable at 3/4-full throttle.
I started by removing the anti-siphon valve and checking its operational. I then replaced the high pressure pump on the fuel cooler with a brand new unit. The boat worked flawless after doing this for the past 3 or 4 trips out. Recently, it started again.
I've noticed that when it bogs, two things are pretty consistent:
1) The tank is usually near full or near empty
2) The fuel gauge will drop completely to empty, then back to full again.
Any ideas? I'm about to replace the 2nd pump at the fuel/water separator. I had it at a shop here locally, but they could not replicate the problem with it out of water.