I did this job on my 06 T5 AWD, too. It was "worst case". Several studs were broken, with 1 broken flush with the head. Also, the manifold itself was warped quite a bit (this is actually what causes the studs to break to begin with). I pulled the cylinder head to do the job. Extraction of the broken studs was done fairly easily on the bench by welding a nut to the broken studs. The heat from the welder really helps a lot. And then you have a nut to turn, and presto - they are out.
The manifold surface of the cylinder head was flat, but the manifold itself was warped pretty excessively. Too much for me to feel good about just bolting it back on. I want to say it was 1/16" out. Yeah. I plugged up all the runners with greasy rags and put plastic bags over the cold side and CHRA. The v-band area was pretty rusted and the turbo CHRA would not release from the hot side. Took the whole thing to a machine shop and they were my heroes and resurfaced it with the turbo still attached!
In your case, I would probably give it a shot to do in place. If you can get the studs out, forget about the possible manifold warping and just get it bolted back together. That will likely be good enough for the rest of the life of the car. If possible, I'd recommend zapping the ends of the studs with a MIG welder if you can reach. This really helps free them up.
If you haven't seen it already, here is a thread with a lot of discussion about this repair. Around page 6-7 I posted photos of my repair steps:
Hi all talking about that squealing issue on other post made me actually talk to my mechanics and book a day to have this sorted. I was asked to organise those parts below and drop the car to them in apx 2 weeks. - Exhaust manifold gasket - exhaust manifold studs - gasket between turbo and...
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