Ok, so I have twin 525efis in my Baja 36 Outlaw. I suffered through a couple header failures like many others. After the port motors header failed 4 hours after a rebuild due to the previous header failure, I gave in and bought two sets of Hardin marine headers. No problems since. During those four hours, I noticed that the recently refreshed port motor was pulling harder than the starboard. I figured while I had the port being rebuilt under warranty, I would anty up and rebuild the starboard one. Full top and bottom rebuild. Since I had two fresh motors, mechanically, at least, I figured my recent uneven power issue would go away. Surprise, it did not. The dealer and I spent hours troubleshooting. The only thing we could find different between the two engines, besides 400 rpm was the timing was about ten degrees shy on the weak motor. After banging our heads against the fiberglass for weaks I gave up and said I'd just run it for the season and see if anything happens. I put on about 20 hours last season and no change. Put the boat back in this spring and no surprise, status quo. In troubleshooting, I did replace the crank position sensor and intake air temp sensor. No change. Since I have twins, I can swap parts motor to motor to troubleshoot. I also have the diacon software too. Any ideas? Both myself and the local Merc Platinum dealer who sells and services a lot of 525's are stumped.

My suggestion would be to run the Diacom software scan and graph and save some inputs from both engine from the, 1. MAP readings at different rpms, 2.TPS position sensor voltage and percentage throttle opening, 3. engine coolant temps, 4.exhaust manifold water temps, 5.oil pressures, 6. coolant water pressures and 7.timing at various rpms (every 500) and take readings and record from both engines and then compare. The PCM 555 on these engines will and can adjust timing based on inputs from these other readings and the retarded timing from sensor input differences will make obvious differences in the way both engines run.
Hopefully you will see a noticeable differences in some input between the two engine from these sensor inputs that is causing the timing pullback and power loss.

The only other things I could think of is based on which year engine you have would be either mis-mounting of the crank position sensor with respect to TDC, or a camshaft installed one tooth of retarded which could possibly result in 12 degrees of initial timing change provided the engines cam sensor input will allow that on a HP525efi, not sure it will.
good Luck, hope you find an easy problem and fix.

Best Regards,
Ray @ Raylar

Do you have stellings extension boxes ?

Negative on the extension boxes, just the imcos which raise my x about 1.75". It's slow to plane but runs so nice and flat once it's up. No porposing like it used to.

Thanks for the ideas Ray, I'll work on it this weekend. Hopefully I'll cone up with something.

Well that blows that theory.

I've heard of issues with stellings driveshaft u-joint "noise"
triggering the knock sensor and pulling out timing on PCM 555
units.

The 525hp efi motor does not have many timing tables, and does not have the knock system active, so if you are seeing a lower commanded timing, (scan tool shows this as base spark advance) then the load factor is off. The only timing table is based off of engine load, not manifold psi or temp. So its RPM vs load. The power reduction logic is based off of 5100rpm and it activates a cylinder misfire, continued running at or near this rpm would set the overspeed code and available power would be 70%ish. So I don't think thats happenning.

So why don't you post some numbers and I can tell you where you are. Need RPM and manifold psi and I can calculate load. Also, do you have an external or internal crank sensor system? What model PCM do you have? Look at the bar code sticker and see if its a PCM0308, PCM0101.....

Have you tried switching the PCM's yet? If so, what happen?

Throw out the simple stuff 1st.
Are you sure the propellers are the same pitch/size?
Are the drives the same ratio?
Is one throttle body opening further than the other?
Do both drives trim to the same position when this is happening?