I never have a problem with my car shifting. But when I'm driving for awhile (about an hour) she starts shifting rough. But it's only from around 2000 rpm down to 1500 rpm. If it's above 2000 and shifting just to 2000, there's no problem. But it only happens with it's running for awhile. The engine light comes on and I get a code for p0306 that will randomly come on, then turn off itself a couple days later. Anyone have any idea what this is? I don't know if it's a spark plug issue or a transmission issue.

 

P0306 is multiple misfires on one cylindrr bank (even bank in this case)
Could be due to a bad injector, bad O2 sensor, restricted exhaust.