I swapped at 1999 Mercury 225 EFI 3.0L to a 2002 Yamaha VMax 225 OX66 on my rig. Same boat, same height, same prop. The Mercury runs a 1.75/1 gear ratio and the Yamaha runs a 1.81/1 ratio. Mercury was turning 5800 rpm's at WOT and the Yamaha won't turn but 5400-5500. I would have expected the Yamaha to turn about 200 rpm's more than the Mercury based on the difference in gear ratios and it being the same setup.

The Yamaha runs great, other than that, but its bugging me because the mechanic (and also Mark Croxton) said it should be turning up close to 6000 rpm based on setup (which would mean I needed to re-prop, I know).

I have checked the hotfoot and the butterflies. Butterflies are about 5 degrees shy of dead horizontal at WOT. But, is that enough to knock 500 rpm's off the top?

I also checked compression. #'s 1,2,3, and 4 are all 106-107 psi. #'s 5 and 6 are both reading 100 psi...which I don't understand. There is no evidence of any scuffing in the cylinders, so why are they both exactly the same but 5-7 lbs below the top 4 cylinders? Yamaha mechanic said that difference was within specs and would not cause the difference. He did say it probably could use a decarb. The motor has less than 200 hours on it and I have used ringfree in it since new. Any idea on the bottom 2 cylinders being lower but even with each other?

Ok fellows. I need some advice on where to look for my rpms and why the difference in the bottom 2 cylinders.
1. Low pressure fuel pumps?
2. Decarb?
3. Timing off a little?
4. throttle body butterflies?
5. ?????

Thanks in advance for your help.