It's possible on those three chambers the hand it binding on the ratchet just as the gun goes to full carry up. This could be a slightly oversize hand, so the first thing to do is as you have done, mark the surfaces with marker and work the action, checking to see what you see. Also check to see if the cylinder stop has snapped into the cylinder recess as the binding occurs, pretty much pin-pointing the either those three ratchet faces as needing a slight stoning, or starting with a polish on the lateral surfaces of the hand, with perhaps - depending on what you see, a slight stoning - slight....stoning of a few strokes at a time, and limit the stone contact to just the upper end of the hand where it contacts the ratchet.
Since you're comfortable removing the side plate, remove the hand and give it a good polish - not material removal, just slick it up on either side. While you're checking, carefully examine the each chamber ratchet for uniformity on the outer "corner" which is trimmed to a flat for the hand to ride up alongside.
Next consider applying a tiny daub of Clover compound to the outer ledge of the of the ratchet, with another tiny daub on the hand slot. Work the action around a few times then disassemble and give the entire suite of parts a good cleaning to remove all traces of Clover compound. Just so you know Clover compound is a very fine abrasive often used for final fitting of 1911 slides and it takes a lot of "cycles" to attain the final fit so it's not an aggressive compound that's going to wear out the gun in a few cycles. You'll probably have to assess for an ease in the binding, then do a repeat. The key is once you've reached your goal, flush all parts to ensure no compound remains.
You could have a situation where the cylinder has been locked by the cylinder stop just before the hand finishes carrying up along side the ratchet and so the hand is binding a bit to squeeze up past the ratchet "corner" for lack of a better word. Remember, S&W cylinders achieve lock, just prior to full cock which means the hand is still moving and must have adequate clearance in the slot with the ratchet pressing.
One other thing to check as you observe the cylinder rotating is how far the crane flexes outward by the hand during cocking, and whether it appears the crane returns to it's proper position on those three chambers, or a tiny gap between crane and frame exists.
Finally, you could just decide to send it off the S&W and let them do the work, because whereas this is the sort of problem I live to fix myself, you really have to understand the parts and how they work - should work, and what you'll see if they aren't working.
