earlwb

I forgot to mention that one could thread some aluminum rod for the muffler holes, screw in the rods using red locktite. The rods are now plugs. Let it sit overnight so the red locktite cures real good. Then redrill a hole or two where you want them, and then tap the hole or holes to match the engine's screw holes. A number of engine manufacturers have done this before and it is a common repair technique too. The plug doesn't have to go all the way to the bottom either, just real close. You want it flush with the mounting surface so that it is easy to make a punch mark to drill the new offset hole and tap it.
Since you are about 2mm off, you could do it to one hole so the muffler threaded holes match the engine's through holes.