New lifters, pistons, rings and all things associated with those jobs will be covered for the full PT warranty, at least that's the way I understand it (I had all those done). Also the way I understand it (correct me if I'm wrong) is if you have PT work done at 99,999 miles, those parts are warrantied for another 12K.
I dont think they will replace the engine unless the block is somehow damaged. My MPG's did not change from pre-work to after work, as a matter of fact they are really good with the BBP tune I have and the AFM off.