Avoid welding next to the cylinder machined surfaces; heat and precision don't get along well.

If enough aluminum is there, tap a higher size and replace those silly bolts by stub-bolts.
Let the steel nuts take the beating, instead of the soft aluminum threads.

Steel into aluminum threads are a one shot deal, more than that and the proper fit is gone forever.
For extra insurance, fix the position of the nuts with tie-downs, conformable washers or any other mechanical method.

Eliminate soft and thick gaskets.

Soft-support the muffler at its opposite end if possible; that liberates the bolts from a good deal of stress.