Who's to say all your rods are the same length ???

I don't know how you did it but I would do this...

1) assemble the short block
2) clean the piston tops in the quench area and put a dollop of putty on each
3) spray wd40 on the heads so the putty won't stick
4) install the heads WITHOUT shims or gaskets (you know the pistons are not going to hit so why do you need shims ???)
4) crank the motor over slowly ONCE
5) take the heads off and check the putty