Regarding the air pocket you will have with a non-horizontal wheel cylinder, I don't believe you will have a problem if you do a proper brake bleeding. The small amount of air will be absorbed into the high pressure brake fluid, think carbonated drinks.
Pump the master cylinder increasing the fluid pressure and then bleed. You'll get most of the air entrained fluid out. I like to keep a newly bled system pressurized over night by blocking between the front seat and the brake pedal; and then if spongy, i.e. air is in the system, bleed it and re-bleed.
The bleed valve in the picture below will be in the same circle as the brake line but is hidden.
