All the info you need is right in front of you. I don't see what is confusing about it. Everything is labeled and color coded. Just connect everything and go with it.
3. The switch diagram shows the brake switch connecting directly to the signal switch. Does this mean that the brake lights now run through the signal switch? If so, is this a problem?
No, that is not a problem, that is how it works. When left turn signal is flashing, right brake light comes on. And vice versa.
