Do you mean a 2004 250 EFI or 250XS? The 2003 & 2004 250XS had the 5850 warning and 5950 limiter. There seems to be an opinion that the 2003 to 2005 XS motors were stronger (they require premium fuel) but I have not seen any dyno pulls on the later XS motors. Can't answer that question with any facts.

If the other motor is an EFI, they are very easy to mod and tune for more power (hood scop mod, mixture tuning, timing, etc.)

The XS motors lose power very rapidly after around 5700 RPMs, and on fast boats run the best speeds propped to turn 5500 to 5700 RPMS.

You haven't listed your current setup. (GPS speed, prop type & pitch, lower unit type and gear,RPMs with each prop, propshaft height).

For instance, if you are running a sportsmaster lower on your rig you will lose 3-5 mph.

List your current setup.