Are the two weird deck height pistons on the same rod journal(throw), IE 1&2,3&4 and so on? If it is it may be the stroke on that journal, if they are not on the same rod throw then it is probably the rods being two different lengths I see that more than I like on new rods
As far as the minimum quench I would shoot for .035 at the edge of the pistons and rock the piston over to each side of the cylinder walls and measure the deck height out there at the cam and outside block sides on every piston at the highest point I would try to have a max of .050 at the highest point also