A third possibility for EGR
A third possibility for EGR related misfiring is clogged EGR passages in the intake manifold. My 2010 Prius got so bad I was afraid to run the engine, it was about to jump out of its mounts. Trouble codes were all 0300s pointing to ignition. I replaced the coils and the plugs to no effect. I never got a EGR related code. I finally removed the intake manifold and found all four EGR passages clogged with a black and brown carbon/synthetic oil tar mixture that was quite difficult to remove. Removal did the trick, however, and the Prius is running fine now. So there's your third possibility for EGR related misfiring.