What prop are you running? I've heard this engine is finicky about being overpropped.
Is the head hotter or colder than normal? Cool would indicate rich, while hot would mean lean and would explain why it has to sit for a few minutes before it will start again.
I can't imagine muffler pressure being high enough to force so much fuel into the engine that it floods out and dies. Even engines that are running super rich to the point of missing a lot of ignition strokes will still keep running.