First, use a punch and hammer and try to work it around. The punch will catch and the shock from hitting it sometimes breaks it free.
2nd Use a flat cutting wheel like the ones with a dremel and cut a slot that a LARGE flat head screw driver will fit in.
3rd, Grind the head off flush and take the TC inspection cover off.
You can then use a pair of vise grips(be patient)and try to get it out of the bellhousing. If no worky, take a propane torch and heat the bolt and then spray the joint where the bolt meets the bellhousing with PB blast. You may have to apply a little more heat and PB(you'll see it boil), then the stud will break free. Had to do this on mine after a torx stripped.
Blake
PS How the heck did the tranny come out with the inspection cover in place? I mean, how did they get it off the flywheel? Unless they pulled EVERYTHING at the same time....