You need to find your low piston and your high piston and swap them on the rods and see if you can get your pistons close as possible. I have done this on many occasions and it does work most of the time.
Yup. This shows up incorrect crank indexing, a different length rod, different compression height piston or a piston head difference. When you get down to measuring THOUSANDTHS of an inch, there's no telling what you'll find.
