Did you measure the deck clearances on the cam side or the motor mount side of the block with your depth mike?
If so or not how about the measurement over the wrist pins?
I use to rock the piston from the inside to the outside and average the measurements until I had pistons touching the cylinder heads at .035 average, which was less than that at the max deck height on both sides of the pistons
I actually needed a minimum of .035 from the highest point
Make sure you measure all eight pistons, especially if your using stock rods Which I see now that you did
I've seen .017 differences in deck heights on several builds using stock rods
Looking at your measurements I would probably swap #1 and #7 piston and rod to see if the deck height differences are in the rods and pistons or on the block machining