93 SJ runnnig really rough after dumping

93 superjet is runnung really rough at idle an on throttle. Carb is rebuilt and did not help, don't think it is plugs, have tried new ones. don't think it is fuel. where is the next place to start looking?

thanks
 
Didn't sink it, after i dumped it, it started up and ran fin for about 100 yds the slowly power went down until it died (didn't see water in compartment at that time). it would fire and run for a while but rough and no power, had to tow back in. at the dock there was a couple of inches in the engine compartment but not in the engine. drained compartment got it fired it would idle rough and on throttle. has been same ever since. changed plugs, gas seems fine. carb is rebuilt.
 
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