Hey, the rivets aren't a bad idea! you could rivet some sheet metal to the hole, then use the spray undercoating to seal it. That saves you the hassle of making the metal fit it perfectly for welding, you just bang on it to fit as you drill and rivet.
That way, the sealed up hole keeps the snow and wet out.
On the other hand, if you want to just cut out the rust, spray the undercoasting on, and put the skirts back on, that should do for now as well, and even though the snow and rain will get in the hole, it will also let it drain out.
As for the muffler...hm. It may actually be a worse job to try and seperate the muffler from the pipes depending how much they are crushed with the clamps. You might get lucky and be able to spray some WD-40 or penetrant in there and be able to bang it off.
If it's a 25-26 inch long muffler, the Thrush will be shorter and you'll need that piece of extension pipe on the front or back to make up for it. The good news is you don't need to worry about hangers since the rear pipe has the stock-type welded to it already. Is the hanger welded to the pipe or is that where it's making the clanging noise?
Before that though, does the heat shield come off the muffler? Maybe you can grind off the spot welds of there are some holding it on and see if that takes care of the noise?
I would hate to advise you to do work replacing the muffler if it's in good shape otherwise and is the same S-flow design as a Walker/Thrush/Dynomax. Hell, it might even be a Walker muffler thats on there. Maybe you can see a stamped part number on it to check.