You could try the route of having a bod shop do one section of the car at a time. Like front clip, then maybe doors/hatch or trunk, then maybe the main body itself... and of course then a trip for floor pans and that good stuff. Just make sure you remember the paint code and it will look alright.

But body work is expensive to say the least, I had a hole in my hatch cut out and a new piece of metal put in.. (maybe 8x4 inches) and a little rust work done on my lower drivers side door, even thought that was just a cover up on the door. It cost about 750.

 

Well the whole car needs to be repainted. Its original factory paint from 88. But thats a good idea to get one part done at a time.

 

The floors aren't bad and in my opinion i dont think my under body is bad either. But i dont know how bad is "bad" when it comes to under body being rusted.. Living in canada its next to impossible to have a rust free underbody here.. pretty sure the 2009mustangs already got rust from sittin on the lots haha :P But ill try and get some pics of the underbody and see what you guys think.