Close that gap
Disassemble and moly coat the skirts to take up the clearance. Thats the only thing I can see that you could do at this point. The engine builder will argue until he blue in the face before he admits he made a mistake. You can always say you decided to moly coat the skirts. Might as well gold coat the tops too.
Call JE and ask what they recommend the clearance to be for that piston diameter, for the HP level your going to make. Mabe the engine builder is correct call and see.
Good luck
Hopefully he didn't over clearance the main bearings...the mains are critical clearances to keep the rod bearings alive. I called every one from DLS to RJC to try to pry this info out when I was getting my motor built.
The guy that built my motor use to build the indy lights stage 2 and we had diffrent opinions, he asked why the mains needed to be tight as they call for. I couldn't answer his question so I called everyone and until I came up with the reason.