I did not know that the 90 HP had a cleanable fuel filter. I thought it was not serviceable.
From you description of how the motor is operating...
Most likely the transition ports are clogged on one or more of the carburators. They provide additional after the carburator leaves the idle state and before it gets to full throttle. They are a series of small pin size holes at the top rear of the inside of the carburators.
If anything is going though them now, the Sea Foam might help to clean them out. If not, the carbs have to come off and be cleaned.
Could also have cracks in one or more of the idle jets.
The carbs not being vacuum balanced can also affect the acceleration. Rough idle is where imbalanced carbs are normally first noticed.
Your diaphram assembly may be not working or out of adjustment. It is part #2.
http://www.boats.net/parts/search/H...RTA VIN# BBBL-4800001/THROTTLE CAM/parts.html
It helps with acceleration and deacceleration. If you gently push up on the end of the rod while the motor is idling, the motor speed will increase. That is not exactly the book test, but if it does not do anything to the motor, then you know you are in the right area.
Those are the most likely problems...although there are a lot of other things that can be checked.
Mike