I guess I will have to assume that at some time it worked ok and the prop size is correct for the engine and boat.
Did the Honda tech do a compression test?
How much off was the timing? If it was too far off, the pistons could have hit the valves and bent them....which could affect the compression and run-ability.
If the compression is around 200 or so for each cylinder, the fuel is good and fresh, new fuel filter and no perceived restrictions in the fuel....then it is possible that the carbs have an issue.
Just running Sea Foam through them, will not clean them if there is much of a restriction. They should be removed, disassembled and cleaned (in an ultrasonic cleaner...if available).
Have you tried to activating the choke when the engine bogs down? If the engine picks up, then it is a pretty good indication that the carbs have an issue.
When you said you were trimming.....when taking off, do you trim the engine all the way down....then trim up only when the boat is on plane?
A motor can rev to 5500 when there is no load, even if the fuel is bad or it is only running on one cylinder.
If you are somewhat mechanical, you could do a cylinder drop test, to see if all cylinders are firing....at least at idle..
Run the engine on the hose or in the tank and momentarily pull the spark plug wires off the spark plugs, one at a time. You just need to do it quickly and see if the engine rpm decrease when you do it. It should decrease....if not, then there is a problem with that cylinder.
If running it on a hose, be sure to tape up the small water intake that is located above the prop under the horizontal anticavitation plate. Otherwise, the impeller will not get enough water and possibly burn up.
Hold the plug wire close to the plug and you should be able to hear the spark arcing....as a ticking sound. If no ticking sound, then you have a spark issue.
Be sure to use insulated pliers. Otherwise, you can get zapped.
There are a lot of things that can cause the engine not to get to the proper rpm. It is just a process to determine where the problem is. Generally, it is by a process of elimination.
Mike