Wow!... my house structure is good... but every time I open a wall I get nervous... wires not in boxes.. insulation removed around piping and not replaced. Good luck I think you have opened proverbial can of worms..
When we gutted and remodeled our house several years ago, it turned into a MAJOR project. Now, first let me say that my house was originally built by my great-great grandfather and great grandfather back and they started in the the late teens and built it room by room until into the early 30s, and we all know what happened to rural America during that period. They used what they had available, which wasn't much. When we gutted the house we found studs made from scraps that were scabbed together..they did the job but weren't the best items, but that's all they had. So we re-studded the entire house. It was a project, but I wanted it done right and wanted it to last. That said, I'm grateful you found that problem in your flue so yiu can make it right and do a proper flue for your stove. Keep us posted!
The Way of an update, just about got the new hearth together and got the chimney in today as well as a bunch of the old one down.
PITA and an expense but a lot of piece of mind coming your way and happy stove. You're sure to get it's best now.