Re: running rough
1. Don't start the motor on starter fluid. Starter fluid does not have the oil you mix in the gas, and therefore you are running without the proper lubrication. Put some premix in a spray bottle if you need to try that route for starting the motor.
2. have you confirmed that you have spark and compression on all cylinders? You may be dropping a cylinder. It would run that way on muffs, but will not run or stay at idle in the water with backpressure.
Are you saying when you open the choke plates, the motor starts to rev up? That would indicate a lean condition, I believe. How did you clean your carburetors? Did you do a full rebuild on them?
Did you set your slow speed needle? There is a procedure in the Top Secret Files for setting the slow speed needle.
Just a few places to start.
Rgds