I have a 2004 Honda Foreman 450 with a snorkle, k&n airfilter, after market exhaust, and have re-jetted the carb. When I hit water or put any kind of loada on the motor the bike seems like it is getting to much gas or to much air, not sure which one but after a couple of minutes it runs fine. Also the bike runs better when it is choked. Any help with figuring out what the problem is would be greatly appreciated...

 

Sounds like you are running lean. I bet you need to clean the carb. Because it runs better with the choke on tells me you have too little fuel going to the engine and choking it reduces the air flow to better match the lower fuel delivery. So clean out that carb real well and see if that fixes it. If that doesn't help you could be getting too much air due to the mods. May need to up the jet and/or down the needle respectively.