I've got Fuel Moto head pipes on two of my machines with CVO muffler cans on them also.
Both have the exact same issues and both are Road Glides, not that (that) makes any difference.
I have pushed the left side in as far as I can to where the cross under shield is barely touching the front flare of the muffler. I have even pulled the right side out of the headpipe to where there is about 1/2" clearance between the heat shield and the flare on the front of that muffler in an effort to even them up somewhat.
There is still 3/8" - 1/2" difference in the mufflers with the left side sticking out that much farther than the right side.
I don't even let it bother me anymore, I just enjoy the ride...... and all that (that) emplies!