I've done something similar twice now with good results... But I didn't bother cutting the T3 flange off. I just used a 1/2" piece of plate steel and milled the openings I wanted, then welded and pinned it to the manifold...
Trick I use is to actually pin it to the manifold first and I stitch weld it on opposite corners about a 1/2" at a time. That and I wait to lay a new stitch in until everything is cool to the touch.
The T4 plate I did for an HX40 about 2 1/2 years ago is still holding up; ran it on my truck for about 40k. My friend runs it on his truck now, maybe only 2k, but a lot of it is off road. I've put close to 15k on this new turbo without issue (did the same thing with this one). I'm sure eventually I will crack the stock manifold or something of that nature, so I'll probably spring for a big foot manifold and see if I can get whoever I get it from to drill it for the goofy bolt pattern of my 451.
I was thinking of just welding the studs in to the manifold and cutting them off. Then drill and tap new holes to mount the turbo. I think there is enough material there to get away with it.