I ended up with a large hole in the cowl on mine, too, but it's my first cowled engine. I was able to put the muffler on after the cowl, however. First I screwed the straight header pipe as far into the muffler as it would go, but still loose enough to turn with my fingers. I turned the lock nuts down to the muffler, too. Then, I placed the header in position to thread into the engine. I turned the header pipe with my fingers so that it unscrewed from the muffler as it screwed into the engine. When it was all the way into the engine, I tightened the lock nuts on both ends. A final tighten on the nuts while the engine was hot, and it hasn't given me any problems yet. There seems to be plenty of thread in both the engine and muffler. It is critical to get the threads positioned right at the engine so that they engage right away, though, so you don't end up with too little in the muffler. It helps to have small fingers!

Steve