Transmission/x pipe Removal ?

Looks like it time for you to get a sawzall and a new x pipe.

Sawzall... maybe, new exhaust pipes.. why ? If you cut the pipes correctly you should be able to have a good exhaust shop put flat flanges in and re-use your existing pipes. Just pull everything appart carefully and then stash the exhaust in your trunk when you get it back together. Drive it or tow it down to the exhaust shop and have them fix you up when you are done.
 
get some bolt/nut removers from sears. they have teeth that grab onto the rounded nut or bolt. its like 30$ a package but ive used them plenty of times now, so imo its a good purchase.

btw make sure you disconnect the battery before messing around the passenger side manifold nuts. i completely spaced this weekend while putting my stock h-pipe back on and woke up to a flurry of sparks.
 
If you can still drive it, take it to the exhaust shop now and have the studs replaced on the manifold before you even start the job. That way you're working with nice new bolts.

+1 No doubt the way to do it. The EZ-outs are a good idea if you have the ability to get plenty of clearance with the car off of the ground. If not, swing by the Ford stealership and pick up some new nuts / bolts and have a shop do it. They shouldn't charge you much to do something like this.