Darrell I went thru what you are doing now run the stock fuel box, and have Eric reflash the ignition box to raise the limiter. Higher compression requires the same air fuel ratio as lower compression and those motors ran on the rich side anyway. If you change airflow then fuel requirements need to be made. I did a lot of mods that Killerbee and Don gave me some tips on. That boat I sold about tens years ago and that EFI is still running today with no motor failures. I found the 250 fuel control to be all wrong for that motor unless you ran wide open all the time
I did not get the symptom of low rpm and surging from the 250 box, which makes me wonder due to the increased fuel flow, it might be running the VST out fuel due to a restriction causing low volume with a increased demand. Might want to look into that possibility
Just thinking out loud
Don also advised me of some earlier 3.0 L that had a more restricted midsection that may require a lower TPS setting in some situations. Maybe he will comment on if this applies to your serial number