I find it hard to believe that sitting for a year would ruin it to the point of them needing to do $6,000 worth of work to it.
If it were me in your position, I would get the engine back, put it on a stand, and start disassembling it myself. Between google, and the rest of the Mustang forum sites, you could easily find any information you needed, and have just about any question answered you could ever think of while doing this.
Once you get the parts off, you could just take the block somewhere and have them inspect it, clean it up, hone the cylinders, etc. You can replace the pistons, rings, and all that yourself. If you aren't comfortable with that, take them somewhere and have them install them for you. The main thing is, there's no way it would cost you anywhere near that much money to do it yourself.