Looking good ! 
So I'm curious as to why you didn't use the already formed pieces from the charger intake and out let and adapt from there ?? Lesson learned when we did the Del Sol years ago. that housing was cast for better flow to and from the charger. if you go to a flat square to a straight 2.5 pipe your killing yourself on flow. I am glad to see your still coming along with this and hope to see it happen one day.So after drilling and Dremel work, I was able to remove the flange portion of the casted portion of the tubing from the Mercedes.
Now I need to make both sides flat, then make a plate to go over it to then braze that and two ends up bead rolled 2.5" tubing for it to be usable!
I also started cutting the gasket for this yesterday in a Fel-Pro sheet.
The space restrictions I have because of the size of the stock part and where they were directed didn't really make sense for the routing I planned. That's what I wanted to do first, but it just wasn't a viable option for the application. However, I plan to not have it square and have it flow better than that, likely not as good as OEM, but close.So I'm curious as to why you didn't use the already formed pieces from the charger intake and out let and adapt from there ?? Lesson learned when we did the Del Sol years ago. that housing was cast for better flow to and from the charger. if you go to a flat square to a straight 2.5 pipe your killing yourself on flow. I am glad to see your still coming along with this and hope to see it happen one day.
That's what I checked first, the rust only goes through the non-structural part, the rest is in good shape thankfully.As long as the rust has only gotten through the outer-most panel, you should be good to do that. If it's into any of the inner panels - which are all high strength steel, then you'll need more intensive replacement to maintain the strength that joint provides.