The last time I had the boat out it was running really good, until I ran out of fuel. I took it out again today and it ran like crap! It was very rough and was skipping randomly. The carbs are beautiful. Are they not getting enough fuel?
My guess is that you sucked up some crap out of the bottom of the fuel tanks. If you have fuel filters, change or clean it. Worse case senerio is that the carbs themselves sucked up the junk, and they will need cleaning.