I think I would fill through the muffler line and use the 3rd line as an overflow. I would plug the third line and then reconnect the muffler line. I had a situation where the muffler was below the fuel tank. If I replaced the muffler line and then plugged the overflow, it would start a rapid siphon into the muffler. Priming by plugging the end of the muffler and flipping is not a bad idea.