sounds like bull because it runs ok when cold.
I think it is something to do with the cold start injectors switching over to the warm state.
you also should reset the ecu by disconnecting the battery for a few minutes or pulling the ecu fuse for a few min. it is a smaller fuse near the center of the fuse box.
any smoke white, black when it is running like crap, do you smell gas comeing out of the exaust?

http://www.bh4wheelers.com/