Check engine light is flashing

Since the cylinders are next to each other , I would look for a common thing between them. Vacuum leak, would be a good place to start. Does the engine have good compression on all the cylinders?. Could be a blown head gasket between 2 cylinders.Look for anything those two cylinders share.

The flashing of the light means damage is being done to the converter, setting that aside...

To help isolate misfire problems, swap parts in question from the cylinders misfiring with the ones that aren't. When the codes shows movement to the other cylinder, you have your bad part.

This isn't always posssible such as a bad head gasket, but can eliminate, plugs, wires, fuel injectors anyways.