Don't modify the hand if the gun works ok using the percussion cylinder. And the fact that it works on 3 chambers with the cartridge cylinder says it's the cylinder that needs to be fixed, not the hand. Modifying the hand could result in problems with the percussion cylinder.
I don't fully understand your description - there is nothing I can think of that would prevent the hammer from going to full cock on half the chambers. Do you mean to say the hammer won't go all the way back, or that the cylinder fails to stop in battery?
If the former, I'm not sure what's going on. If the latter, then yes, shortening the hand would be a likely solution. For those three chambers on that cylinder, but why mess it up for the other chambers? The real problem is in the notches on the back of the cylinder - look for burrs in the notches and file them down.
By the way, you need to keep that percussion cylinder even if you never intend to use it again. If you ever sell the gun you need to sell it with the percussion cylinder installed and sell the cartridge cylinder separately. Technically, when you put the cartridge cylinder in the gun you've 'manufactured' a new gun, which is legal as long as you keep it for personal use and don't sell it that way. If you do, you must buy a tax license from BATFE first. Selling it with the percussion cylinder avoids that little legal issue.