The problem is that the alignment pins were match drilled. You should be able to work them out with some good needle node pliers. Once they are gone the new ratchet should have enough play and line up.enough for you to stick fired cases in the chambers and then drill new holes off set a set of chambers. I have thought of filling the old holes in cylinder with short pins fixed with red loctite, milling them flush, then stick in the replacement ratchet, fill the chambers to align it, the drill trough the ratchet holes, then remove it and loctite new full length pins in place.
The other option would be to drill the holes in new ratchet slightly larger. They are now .050. If you drill them 1/16" (.0625) they may work. They are not intended for positive positioning. Loading the chambers will do that. More than one cylinder has shown to be slightly out of time (not carry up) with empty chambers and work perfectly when loaded
I have messed with quite a few ratchets and cylinders, I can't remember ever finding a ratchet that fit a cylinder other than the one it came with. Those pins are always a bit off.
S&W has not actually improved many things in the last 20 years but way the newer type ratchet mate to the cylinders is an improvement over the 2 pin system IMHO. I can actually swap those from one cylinder to another.
If you get real desperate I have a couple 1917 cylinders.
You could also have a newer model 25 cylinder fit to it. The teeth look different, but the edge the hand works is the same. I have done this, You can even use the big knob off a 1917 type rod, just drill it out and silver solder it on the end of the new rod.
This highly modified 1917 is running a newer 44 mag cylinder reamed to 45 colt and a new left hand thread rod with a big tip soldered over it