2005 Sienna, I occasionally get a p0304 (misfire cylinder 4) and engine runs rough. I found if I replace or clean the spark plug in cylinder 4, it goes away. For awhile. Then if I look in there, the spark plug gets really dirty and black. Compression test seemed to show normal compression in all cylinders.
Seems it was the ignition coil was going bad. I could have sworn I did the test where you swap the ignition coil from '4' with '6' and the same code was there, but somehow, it was the ignition coil. At least, replacing that ignition coil seems to have cleared up the problem for more than a year, same spark plug. Maybe the coil was weak?