You can do a lot with a sawsall and clamps, but it’s such an unrewarding job that employing checkbook muscle may be better use of your time. The trick is finding a competent shop that uses OEM or better materials - many of the chains and cheaper shops offering long muffler warranties provide such poor mufflers you’ll be back in a year, maybe two tops. They’ll replace the muffler for “free” but charge for all the associated pieces.
Plus the labor is never free on these “Lifetime Warranty” repairs!
OK, so I was able to remove the muffler with heat from a propane torch, but the flange on the intermediate pipe is thin and weak, I can’t get a good seal on the gasket because the gasket is 3/16 thick and doesn’t compress. The inter flange has welded studs on it and just bends around the gasket because the flange is 1/16 thick unlike the new muffler flange which is 1/4.
Plan B for me was to cut the inter pipe on a straight part of it and put a connector and muffler clamps. But I think Plan C might be a better option 1st, which is to replace the whole inter pipe. What do you guys think?
So I actually attempted to loosen the nut at the Cat, inter pipe connection and it’s a no go. It didn’t budge and the nut stripped. So I guess I can still undo that connection by cutting the stud off and then drilling out a new hole or do what I said I planned on was to cut the pipe and put a connector with muffler clamps on it. Which is the better option?
Just cut the flange bolts off and replace them. That’s what I’d do, and that’s what a shop would do.
And on all my vehicles over the years before stainless exhaust systems became commonplace, I replaced the old nuts and bolts with stainless steel with a dab of antiseize (the SS in hardware store nuts & bolts galls). I replaced the entire exhaust system in my '89 Toyota pickup in 20 minutes once in a parking lot, start to finish including jack time, because I’d previously used SS nuts and bolts. I was living in an apartment where working on cars was verboten, and I didn’t want to get caught. 
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the_same_mountainbike: I mentioned the connection is stud and nut, not a bolt and nut. Right I wish it was a bolt nut set up because I would have put a sawzall and cut it first. That’s why I ask if it would be ok to cut the stud and drill the rest of it out, the flange hole size is 7/16 so drill bit would be around that size or is it a better idea to cut the pipe in a straight spot and put a connector on it with muffler clamps on it?
If the stud has head but it’s not a hex head, that’s a spline stud. And those can be pounded out of the flange and replaced with a bolt.
But if there’s no head on the stud, then this is how they’re removed and replaced with a bolt.
Tester
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I’ve never had good luck with drilling out a stud unless the part it’s in can be removed and put on a drill press.
I’d suggest busting the nuts off with a nutsplitter and chasing the stud.
Tester: got a pic of what the stud and nut are looking right now. If you can look the stud has a small male end that comes out the other side of the Cat flange, it’s squared. Is that an easier stud to take off or drill out that you are talking about?
the_same_mountainbike: Ya I wouldn’t be able to take it out and put it on a drill press, i’d be drilling laying on the ground under my car. I also have that nut splitter as a loan tool but if I’m able to bust off the nut, the threads are in bad shape, so I won’t be able to screw a nut back on it. Could it even be retreaded successfully, especially in a tight spot?
That looks to me like it can easily be cut off with a cutting wheel, the center punched or drilled out, and replaced with a bolt and nut. Is there some restriction that the photo isn’t showing?