Sounds like you are getting shafted because you weren't completely clear with them what you wanted them to do. Maybe they took it as "Do everything because they keep asking what our recommendation is."

If what they installed is not what you wanted and you didn't sign anything, i'd tell them to take it all back out and keep it. Also, requiring a .040 overbore is sketchy. I'd venture a guess that +.04 pistons is all they could get quickly so they ran with it. And since overheating was a concern, that overbore is only going to make it marginally harder to keep cool.

FWIW, I just picked up a block that I dropped off in November. The rotating assembly took 4 months to ship because Icon was that far backlogged on pistons.