I can get .004 all the way thru from the right side and .007 about half way thru from the Left side. Looking down from the top the cylinder looks pretty square to the frame. But I don't know how easy it would be to see .003 out of square by looking. Might be easier to tell than I think.
I will try checking the timing too like you suggest. Do I need to have the revolver in lock down position while doing the timing (Pull hammer back, hold trigger down while lowering the hammer and then keep trigger held down while checking each chamber?