Let's back up a bit. If the engine was decently maintained it's not an "old" engine. My 2007 model BF 225 has over 1900 hours and still runs great and I can get 5950 rpm at WOT (with out riggers down and less than 1/2 tank of fuel.) Several folks on this forum have put well over 3000 hours on their Honda's.
Let's assume that the throttle linkage is correct and the valves are still within spec. (Personally, I would recheck both.) Obviously, it's firing well and you did not mention anything about missing at the high end. Furthermore, you said that previously you were getting 33 knots when you first got the boat, so let's assume that you don't have a (significant) prop problem at this time.
So what's left is compression, air flow, fuel flow, or a problem with the VTEC system.
You said all cylinders were "10 Bar." I don't understand that. What PSI or millibars were you getting? I don't know the exact specs for the 90, but I think it's around 210 to 215 psi. Compression test should be done on a warm engine, fully charged battery, all plugs out with throttle fully open. Engine should cranked to at least 300 rpm. There should be no more than a 10% difference between the compression on the highest cylinder and the lowest cylinder. If you are not getting that level of compression on the cylinders - at least 200 psi - then a good dose of Yamalube Ring Free (or a similar top quality decarbing product) might solve your problem. Try to hook up a small external tank. I believe the correct mixture for a shock decarb using Ring Free is 2 ounces per gallon. Warm up the engine, hook up the external tank and run enough mixture through the engine until you are sure it has saturated the entire fuel system. Then let the engine sit for several hours before restarting. Most folks will do two decarbs just to make sure they get as much carbon build up out as is possible. You'll need to change your oil after decarbing. Then, re-measure compression.
Btravlin2 just completed this process on the BF 225's that he is restoring, so he has a lot of recent first hand knowledge.
Air flow- I can't help much here. Just make sure that your air passages are all clear. I recently had a problem with the intake air bypass (IAB) control on my BF 225, but I have no idea where or how that works on the BF 90. If it is not working properly, you will lose top end performance because the cylinders are not getting enough air through the intake valves.
Fuel flow. Have the high pressure and low pressure fuel filters been changed recently? They should be changed at least annually. If you have an external fuel/water separator (which you should) has that filter been changed recently? On the Honda fuel injected engines, there are a couple of "hidden" fuel filter screens that tend to get clogged. On the BF 225, one is under the high pressure fuel pump and has been the source of several performance problems with BF 225 owners. I suspect the are also present on the BF 90, so they should be checked.
VTEC system. Again, I can't help you on the BF 90. On my BF 225, the VTEC kicks in at 4600 rpm. If for some reason it is not kicking in as designed, then you are really operating with a 75 HP motor. There are tests for determining whether or not the VTEC is working properly, but again, I'm not familiar enough with the 90 to give you any directions down that path.