1. I think the 56cm would suit you better since it has a shorter top tube than the 59cm.
2. Yup, throw a cog and lockring and you'll be set.
3. Levers choice depend on how long you stay at the flat/horn part.
3b. That's sounds really wide...you should try to measure it again.
4. Go with 165mm, no doubt about it.
5. Stock Mark V has a 46t chainring, 46/16 would be a rather tall ratio..it really depends on the terrain you live in and how strong you are, I live in a hilly area and I find the 46/17 slightly too tall for my liking. I've got 44/17, which is the perfect ratio for me.
6. Stem length depends on your reach, you'll be more stretched out with a longer stem and you'll be more crammed with a shorter stem...you decide.