As I said before compression , spark, and timing can be tested.
You need to test them to rule them out.
The ignition system has testing procedures in the manual so you can test voltages into and out of CDI even while problem is there to see if spark is the problem
If nothing is found wrong with them them you are left with a fuel to air ratio problem.
Too much or too little fuel will not let a cylinder fire and burn the fuel properly
Fuel pressure and vacuum can be tested, look here to find some good reading on all sorts of things
http://forums.iboats.com/forum/engin...-questions-faq
It is a possibility you have an air leak into the fuel system and you motor is running out of fuel
Fuel pump leaking into #3 crankcase will affect only #3.
There are seals at the top and bottom of crank and seals between the cylinders on the crank. lets hope they are not a problem.
I am fairly sure that your 3 cylinder 90 has recirculation check valves on the block/ crankcase like my C40. I found 3 of the 4 bad but it did not have a problem like your motor.
Test what you can to make sure and move on to other things
I had a problem with high speed miss on my 3rd hand C40 when I 1st got it.
Ran well if I took the cowling and silencer off and ran into the wind only.
Took me close to a year to finally figure out someone had drilled out the main jets
Replaced them and it is good to go now.
All you can do is test everything properly and eliminate what you can