I didn't expect the barrel to time up correctly, but it should screw on without being overly tight. I think the exposed threads on the barrel might have been rolled over a bit, probably bumped or something similar, running a die over the threads should clean them right up without problems. I've heard that the old Colt barrels used what was essentially a pipe thread, so a tapered thread probably shouldn't screw on without a bit of alteration to the threads. A darned good old time gun smith I knew would take revolvers that shot right or left and smack'em with a rubber or leather hammer to bring them on target. He said there was a lot of slop in those old barrel threads.
I'm glad to hear that this is a very strong action, it makes it worth repairing, Since the gun is getting a barrel job I'll probably have it blued so the parts match. Bluing won't hurt this old gun, she's far from a collectors item and it's been reblued once already.
