When I had water in the tank it would start running rough and I would have to pump the throttle to keep it going. Eventually it wouldn't run at all. The final time before I fixed it for good, the boat stalled on me in the middle of the lake. I pulled the rubber fuel line off the pressure side of the fuel pump and put it into an empty plastic pop bottle. I hit the starter for numerous short bursts until most of the water was pumped out of the tank. Eventually I got the motor running before the battery was completely dead and got back to shore.
Your problem may be a bit of water but it sounds more carb related. I might want to check the power valve in the carb even though it's been rebuilt. Is the carb the stock Holley 4160? There are other culprits to track down too -- vacuum leaks, choke sticking, sticking floats (although that usually causes flooding),
2005 X2, Viper Red, MCX, OJ TZ-X5 prop, PPass, rear 750 sacs, KBS, IBS, Bennett Wake Plate, custom wake shaper
(previous) 2001 X5, 1991 TriStar 190