The Following information is the routine I use in discovering where a fault lies, it is quite generic and applies to most outboard motors, once you have read the information and found that a fault is still residing on your engine please let me know and we can move forward onto other possibilities you dont need to press accept until you are happy with the answer and you can keep the question open until you are happy.
First you need to diagnose what the fault could possibly be, First checks to always undertake
would be a spark test and compression test, this will rule out an spark problem and a serious
The spark test should always be done with safety in the forefront of your mind
the flywheel is spinning and can do a lot of damage,
remove the plugs from the cylinders get a good source for grounding them on the engine block and make sure that they stay grounded, if
the spark is not allowed to go to ground it can feed back through the ignition system and damage
the Ignition, crank the engine and ensure that all cylinders have a bright blue spark,this test
can also be done with an inductive timing light(with plugs left in) or a "glass" spark plug
which plugs between the HT lead and the plug, whilst doing the spark check with the plugs removed
you can put a compression tester onto each cylinder and check compression, compression should
always read over 100psi and within 15psi of each cylinder, if the readings fall outside of these
figures then the chances are you will need to have the engine overhauled as some internal wear/
damage has occurred, an engine with all 3 cylinders at 90psi can still idle ok but will not develop
the HP required to run efficiently,if the spark and compression tests come back good then you can
assume that the fuel system is where the problem lies, firstly check that you have good fuel and
not contaminated old fuel, modern fuels only have a shelf life of a couple of months before they
start deteriorating so if you are using last years fuel this can cause problems,if the fuel is good
then your next thing to check is that all fuel lines up to and including the engine are in good
condition with no cracks splits or poor connections,change the fuel filters as they can block and
restrict fuel flow, check your fuel pump diaphragms as any splits or holes will cause an engine to
run inefficiently, if you have a hole in a diaphragm the fuel will usually pass straight into
the crankcase and "over fuel" the engine this is because most fuel pumps are vacuum driven directly from
the crankcase pressure. If all these checks are sound then move onto the carb/s the carbs will need to
be removed, stripped and cleaned, I use a product by Quicksilver called Power tune to clean the carbs
this product dissolves salt residue and the "varnish" just spray it all over the carb components leave for
a few minutes and spray them clean, I dont recommend the use of high pressure air lines as this can
sometimes push a blockage further into a recess and cause more problems, if the blockage is very bad then
you could take the carbs to a specialist who has an Ultrasonic Cleaner In an ultrasonic cleaner, the object
to be cleaned is placed in a chamber containing a suitable ultrasound conducting fluid . The main mechanism
of cleaning action is by energy released from the creation and collapse of
microscopic cavitation bubbles, which break up and lift off dirt and contaminants from the surface to be
cleaned. The higher the frequency, the smaller the nodes between the cavitation points which allows for more
precise cleaning. The bubbles created can be as hot as 10,000 degrees and 50,000 lbs per square inch, but
are so small that cleaning and removal of dirt is the main result.
Whilst the carbs are off check the Reed valves on the inlet manifold for cracks breaks and even a reed missing completely the reed valves are to help control when the fuel is drawn into a cylinder if one has broken you will need to investigate to ensure that no internal damage has happened to the engine this will usually show up on the compression test with an abnormally low reading ie below 100psi.
When you reinstall the carb/s if you have 2 or more you will need to ensure that the carbs are synchronised this is vital to the idle of an engine basically when you put the carbs back on and adjust any idle you must ensure that all the carbs butterfly's are completely closed at idle, this ensures that a cylinder is not trying to run faster than the others or vice versa.
I flushed the carbs, cleaned the spark plugs, but i haven't had time to clean the filter element (really hard to get to) etc. My guess is it's probably one of the things you mentioned, but i won't know until late July when i'm back on the coast. Since you were kind to help, i'll give it the benefit of the doubt. thanks!