Actually, replacing the muffler section shouldn't be all that difficult for any decent welder or muffler shop. You can buy the muffler sections at Jegs, Summit, and any number of shops, including most muffler shops.
The trick is to make sure you get a nice clean and strong weld and having the turn-outs oriented correctly when they are finished. If you plan on cleaning up the weld by grinding it down and polishing it out, make this clear to your welder as you need enough material to grind without weakening the weld joint.
If you plan on buying a set of sidepipes, I would heartily recommend the guy who built mine. All his welds are ground down and polished out, his transitions and collectors are meticulously cleaned up so they look like they are one piece, and he'll make them in any configuration you need. Right now he builds sidepipes for Factory Five, Shelby, Pacific Roadsters, Midstates and several others I can't remember as well as some he builds for Finishline. Some of his work on Cobra replicas has been in kit car magazine, among others.
His name is Len Ewell and his contact is
len@boffinMS.com or call him at 503-624-2659.
Tell him I sent you-
Bob