The new flange fit right up! I cut and bent a box shape from a recycled computer monitor brace, because I didn't have any other thin plate steel on hand. Then, I drilled the stud holes and a slot for the port. I ended up with an opening slightly smaller than stock, but it didn't decrease performance enough to bother me.
I may have to open the flange port a little wider after a few more rides, but it performs well enough to leave it be for now. I want to make sure it will hold up before taking much more material away from the plate.
The new port box slid over the header tightly and bolted together easily. I considered welding it, but that would be a real problem to remove in the event of another flange failure. Very happy it allows me to use the newly constructed header and Briggs muffler again.
It took some brainstorming and a few hours of metalwork, but it should be worth it in the long run. Hopefully, this is the last exhaust project for number one.