I did some more looking at the gun, with the percussion cylinder in, and the pistol at half cock, the ram did not fully line up with the bottom cylinder and the bore was off just a touch. With the conversion in place, the hammer was just missing going to full cock on 3 out of 6 cylinders.
It appears that the depth of the grooves on the conversion cylinder is a few thousandths less then those on the percussion cylinder.
So, I took it apart, and inspected the hand and other parts. I found a few machine burrs on the hand where it engages the cylinder, I lightly filed the burrs off and took a fine stone to the rest of the top of the hand to clean it up. Again, the only real metal removal was the machine burrs. The rest was polishing.
Once back together both cylinders line up properly and the revolver now fully cocks on all cylinders for both the percussion and conversion. The loading port lines up now at half cock also.