Howdy
I have an old brass framed Uberti Navy that I bought back in 1968. The muzzle on it was also cut our of square. I would not worry about it.
I have a pair of Pietta 1860s. I bought them a few years ago when they were on special at Cabellas. Frankly, and you are not going to want to hear this, I wish I had spent a few bucks more and bought Ubertis. In my opinion, Uberti does a better job fitting and finishing their BP revolvers than Pietta does. Your out of square muzzle is testimony to that. I was also less than pleased with the amount of burrs that Pietta left on the frames prior to case hardening. Once hardened, the burrs cannot be removed without leaving behind a mark.
As far as what to do to prepare it, the very first thing I do with any gun that I intend to shoot with nothing but Black Powder is to completely strip it down and remove all traces of factory oils and grease. I usually use lacquer thinner or paint solvent. No, it will not hurt the blue or the 'case colors'. I strip all the parts to bare metal, then I relubricate everything with a light coating of Ballistol. Ballistol is completely compatible with Black Powder fouling, not all petroleum based oils are. Then I put it back together again.
OK, I have one of my Pietta 1860s in hand. The condition you mention about the cylinder not going to battery until the hammer has been pulled back past full cock is very typical of many revolvers. No, it is not ideal. Ideally, the bolt should pop into its locking notch at exactly the same time as the hammer goes to full cock. The alternative is that if the bolt pops in place before the hammer goes to full cock, the hammer will never get to full cock. The hand will wedge the hammer from going all the way back. No, you should not install a longer hand. Just remember to give the hammer a good yank every time you pull it, so the cylinder always locks up. Alternatively, you could lengthen the hand slightly by peening the end with a center punch, but the hand may be slightly hardened and this may be difficult.
The problem of the bolt popping up too late has nothing to do with your hand, it is a timing problem with the bolt and the cam on the hammer. Ideally, the bolt should pop up about halfway into the lead in to the locking notch. That way, its impact will be absorbed by the full length of the lead in, rather than striking the edge of the notch.
Guess what? both of my Piettas do the same thing. I have run into plenty of Ubertis that do the same thing to. This is something that is probably beyond your expertise. With all due respect, the bolt is not too wide, it is popping up late. If it was too wide it would not fit into the locking notch and the cylinder would not lock up at all. Basically, the bolt leg is falling off the hammer cam just a little bit late. Adjusting this means either adjusting the hook on the bolt leg, or adjusting the top corner of the hammer cam.
Before you start filing, you really need to understand the relationship of the hammer and the bolt. It is complicated.
Frankly, with my Piettas I have not bothered, I just let the bolt rise late.