Marlin,
I am not the one to give any advice on welding, because almost anyone can weld better than me and knows more about the art.
Everyone here knows more about a Cub Cadet than me.
What I can tell you is that the back of the muffler box on the 1250 Nightmare looked about as described. I didn't want to deal with it, either. First, I bought a muffler crutch from David Kirk and installed it. That was a very good investment. Then, I cleaned all the cracks and cracked areas with brake cleaner, degreaser or something. I did a final cleaning with starting fluid. I let it sit overnight to be sure everything was dry, and applied JB Weld to the cracks. More than a year later, it is still holding; the fumes that were wafting back at me appear to be going where they are supposed to go and the muffler box seems to vibrate a whole lot less.
From my prior postings, you know I have had a lot of trouble with vibration. After several tweeks over time, I finally have a happy medium with my motor mounts and I believe they are doing what they are designed to do. There has been no further cracking or deterioration of the muffler box backing plate since the JB weld was applied.
Good luck. This is just my 2 cents. I probably couldn't get it to work again in my lifetime.