Excellent information, this helps!
With cyl removed, the hammer is allowed to go back further and therefore fully engage the sear. So the sear and the hammer slot are OK.
It has to be the cyl pawl (hand). I know you didn't change the pawl, but the slight variations of the pawl mounting hole location between hammers can make the difference.
As you said, the cyl is binding because it locks up before the hammer is fully cocked. Take a tiny bit off the front point of the lower tooth of the hand. Just remove the cyl, don't diss-assemble the gun. Stone or file the upper front point on the lower tooth of the hand. Put the cyl in the gun and see if it cocks. If not take a little bit more off.
Once you can get the hammer to cock with cyl installed, you'll have perfect timing. The cyl will lock at the same time the hammer cocks.