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),
"For every complex problem there is an answer that is clear, simple, and wrong." (Henry Louis Mencken)
2005 X2, Viper Red, MCX, Acme 1285, PPass, rear 750 sacs, KGB, IBS
(previous) 2001 X5, 1991 TriStar 190