5.7 paired with 5.0 290 AJ

Due to t he difference in cubic inches alone, the torque curve will be different. You will not be putting out the same HP and Torque for the same RPM. Not sure if the difference would be noticed much, but to properly sync your motors for the same output power, you will be at 2 different RPMs. It would not hurt anything, but it would drive me crazy knowing they were not the same.
 
Lazy is right about the HP ratings, but if your boat is a 2000, you have 240 hp 5.0 EFIs (throttle body injection). My 2001 was "born" early in the model year and has those engines as well. The 5.7s of that era were also throttle body EFIs and rated at 260HP. When merc went to MPI (multi port injection) the 5.0s were bumped to 260HP and the 5.7s were dropped out of the 290AJ. If your ECMs, throttle bodies, injectors, etc. are in good working order, I would think it would be much cheaper to go 5.0 or 5.7 longblock and swap over the intake, etc. (I assume all that stuff would work correctly with a 5.7 but don't know for sure). My starboard engine tuliped a valve with 100 hours and merc (under warranty) supplied a new long block and the swap was pretty straight forward. Moving into anything with MPI would mean longblock plus all new electronic controls, sensors, fuel delivery, etc which I think would be way more $ (but also way more HP!). Lots of options. Good luck!
 
Before you pull a motor, I'd diagnose exactly what's going on with the current engine. Clearly blue smoke is not a death sentence. I suspect you are running rich, especially if the compression is good. Next up would be a leak down test that would let you know the condition of the valve train. It could be that your guides need replacing. You could pull the heads in situ and any self respecting machine shop could machine the heads and press in new guides for probably about $350-400 per head. Certainly a lot cheaper than a re-power. Unless you starved the engine of oil, the lower end should be fine.
 

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