Try swapping the ignition modules and see if the misfire follows it. I had a similar situation with my first 12. It eventually stopped firing at all.
Wag Aero Sport Trainer built,sold and wrecked
N588DF RV12 #336 built, sold and alive and well in New York
N73DF RV12 #244 built, sold and alive and well in Florida
N91 RV RV9 I wish I could say I built this one! Mark Santoleri hit the ball out of the park on this gem.
Currently restoring a 1978 Citabria GCBC