The Dixie Gunworks catalog says you should use .451 dia balls in their Pietta reproductions and .454 in the Uberti's.
I lean towards the .454 in my .44 cal guns as the balls seem to be a little tighter in the cylinders so they don't walk forwards during recoil as much as the smaller .451 balls.
Wads are up to you. Some say they improve accuracy and assure a flame proof barrier to lessen the possibility of chain fire.
Others say they cost about as much as the balls and aren't worth the extra expense.
These wads by the way may be hard to find. Ox-Yoke, the company who made them is out of business, the last I heard.
You should be able to use your #11 caps, but if they are too loose, you might want to try some #10 caps.
Yes, the nipple wrench for most rifles is too large to reach down in the little counterbores on the back of the cylinder so you should look around for a wrench made for pistols.
Happy Shooting!
PS: Most C&B guns shoot high. Of the many I own, only 3 shoot to the point of aim. If your gun doesn't have adjustable sights (Colts rarely do) it is something you will just have to get used to, but it is Historically correct as near as I can determine.