"Eyeballing" cylinder alignment often isn't valid. It's not unusual for there to be an optical illusion that looks like the cylinder isn't aligned.
The only valid test is to have the gun checked with a range rod.
This is a precision sized rod that's inserted down the bore.
If it refuses to enter the chambers, the alignment is off:
http://www.brownells.com/aspx/NS/sto...20RANGE%20RODS
If the gun really is out of alignment, a good single action qualified gunsmith can adjust it.
If you're 100% SURE it's out, buy a copy of Jerry Kuhnhausen's book, "The Colt Single Actions: A Shop Manual".
This is a real pistolsmiths book on single action repairs. This will tell you exactly how to check the gun and how to repair it the right way:
http://www.midwayusa.com/viewproduct...tnumber=133799