Brother-in-law had a similar problem , and had to extend the tail pipe hanger, on his 05 Tiffin, burnt the carpet in one compartment .
Now this is JMHO.
There is a lot of weight involved in the length of pipe and I doubt that the do-nut and bolts at the exhaust manifold are the only things aligning the pipe, Should be hangers at the cat. convertors and mufflers to stop the pipe from contacting the body. Now the pipe may have been damaged/pushed up to contact the body, most likely cause, in that case the pipe would have to be heated to re-align.
If you can't hear an exhaust leak then I don't think replacing the do-nuts will cure your problem, I think a second oppinion ( muffler shop maybe) is in order.
Should have said this first... Welcome to iRV2 .
99DSDP 3884, Freightliner, XC, CAT 3126B, 300 HP /ALLISON 3060
2000 Caravan toad, Remco & Blue Ox.