Could be the coil is starting to go bad. They usually exhibit their first symptoms when they're hot. A weak/intermittent spark can cause rough running. When it's cold, pull one of the spark plug wires and hold it near a good clean ground and crank the engine and see what a good spark looks like. It should be bright blue/white and jump at least a 1/4 inch gap. Then, once it's warmed up and started to run rough, do the same thing and see if the spark has degraded to a more yellow color and won't jump as large of a gap.