Another thing to check,
The big end of the rods have a chamfer. The rod bearing is also offset away from this chamfer slightly. The chamfer always goes toward the 'fillet' of the crank. It could be a few of the pistons are installed backwards and the rods are binding because of this.
Put a GOOD straight edge on the crank webs in the block too.
V-block the crank and check run-out.
Mic each bearing and journal.. As mentioned, plasti-gauge..