Hi PJ,
Unfortunately, Pettifogger is spot on. The absolute FIRST THING to do to an Open Top is check and correct the Barrel/Arbor fit. If that isn't right, he gun will never be "right."
Take it apart and assemble the barrel to the frame without the cylinder. With the barrel turned off to one side install the barrel without the cylinder. It should seat with MINIMAL effort. Then turn the barrel into alignment with he frame. The pins are in the way. But, the barrel should twist until it slides up against the pins. If it hits he frame, you have some work to do. If it hits the frame, I'll refer you to Pettifogger's articles pinned on The Open Range.
Once the Barrel/Arbor fit is correct you can move onto head space and end shake. The work already done to the gun will then be worthwhile.
Coffinmaker