Doesn't sound like fuel pump.
Does the boat have throttle-by-wire? ICBW but I think the MCX in 2005 was the only engine with TBW. If no TBW, check and calibrate the throttle connection link and servo spool as described in Perfect Pass's instruction and troubleshooting manual (can be downloaded from PP).
If it's throwing an engine code, it would be helpful to know what that code is. Is it announced in the MFD? If not, may need to see someone with a marine code reader.
'04 MariStar 230VRS/MCX