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KoolBRZ I tried this today and it didn't turn out like I expected. The holes in the flanges are about the same as the bolts so I don't know how you could possibly leave them misaligned to fix the overall muffler alignment. Unless you used thinner bolts?
When the muffler was dangling by the hangers only, I had the alignment perfect. I then slid bolts in and it still looked ok. But after tightening up, it brings itself back to being not aligned perfectly.
It's not terrible I guess, but not perfect.