Suzuki 700 Twin Peaks "2004" runs rough

I have a Suzuki Twin Peaks 700 "2004" I have recently took on water through the air box that completely filled up the belt cover housing, since then I have got it cranked up and reset the sensor that limits it to 8mph and changed oil several times, filter and changed spark plugs, after doing that and riding monitoring performance it would run rough back firing some and all so then moved on to cleaning carbs and after reinstalling them it ran like new, now the problem is It runs rough again and the only thing I did was added a small amount of seafoam since I was told is good for it, any suggestions? last note I have taken out the spark plugs again and checked them they were black so I cleaned them and put them back in still no different. runs great at idle currently just when rev up it tuns rough

Is that fuel injected?

Drain the gas and try some fresh stuff, you may have put too much Seafoam in for the amount of fuel you had in there.

the choke system has debri in valve prbably need new valveandcable

you also could have moisture in your electrical connectors or some crap covering the pick up sensor. it might be able to read at an idle but when you speed up the crank or cam it is possibly getting harder for it 2 read. depending on how it gets its signal.