Re: johnson 9.9 runs better with 1 plug ou
Sounds to me you have lost the operation of the cylinder that you have removed the plug from. If that cylinder is not firing, the motor will run a little better if you remove that spark plug because the other cylinder will not need to overcome the bad cylinder's compression.
That being said, you need both cylinders so I would do a proper spark test. You didn't give the year of the motor so I don't know whether you have points & condensers or a powerpack. Points will corrode quickly after being submersed and that could be your problem or it could be many other things.
Gives us the year and anything more on the symtoms and we should be able to lead you in the right direction.