2014 900xp Rough Start/ide but runs 100% when warmed up

Hey guys i didn’t put my gas cap on right when i was in hatfield last month and water/mud go into the fuel tank. After an hour of riding i guess it started clogging the fuel filter and my rzr started sputtering and stalling. I could start it up and it would run fine for a while until it would sputter and die again. I was able to get the 12 miles back to the cabin doing this. Once i got back i cleaned out the tank and the fuel filter on the bottom of the pump and put all clean gas in and changed the spark plugs. It starts fine now but runs like it has a miss for the first minute or so then idles and drives perfectly. It actually has more power than before. I’m guessing the plugs were bad for a while. Ive been through 1 tank of gas as i was hoping it just needed to clean the system out but its still doing it. Any ideas what to check for?