What a bunch of trouble you've been through on this! In a case like this, who is covering all the extra costs? Did the machine shop order the wrong pistons? Did you provide your own parts? Can you return the "wrong" pistons, or are they considered used now that they've been installed?
You have my sympathy! These jobs are expensive and time-consuming enough without all the problems you've encountered.
Experience is something you don't get until just after you need it.