A. You can stop the deuce without air assist - it just takes a lot of foot power. Per Bjorn's data, with air assist you can get ~1800 psi in the brake system vs ~400 psi with foot power alone. I regularly drive my Deuce around the yard sans air assist while waiting for the air pressure to build up and the brakes work fine, but I am talking 3-4 mph, not 40-50 mph.
B. I wouldn't worry about replacing the M/C or wheel cylinders unless they are leaking or otherwise defective. Same for the AHU (air hydraulic unit), if I ain't broke, don't screw with it (good philosophy for most any part of the Deuce, routine maintenance excepted). The only thing I WOULD suggest is to pull the air pipe off the back of the AHU and give it couple of squirts of air tool oil or similar very light oil into the air chamber, that helps keep the AHU working freely (I use Breakfree CLP, for what it is worth).
C. The AHU (brake booster/power assist) doesn't really complicate the brake bleeding process. There is a bleeder on the AHU, bleed that first, then bleed the wheel cylinders, starting with the furthest from the M/C and work your way in. Just make sure to use the same fluid for make up as is in your system - USUALLY DOT 5 (BFS, or Brake Fluid, Silicone, in military nomenclature), although some do have DOT 3, the regular civilian type brake fluid. If in doubt, take a sample from your master cylinder, put it in a small jar, add some water, shake, then let it set for a while. If the water separates out, your system has BFS. If the water mixes with the brake fluid you have DOT 3 in your system. Either one will work fine, just don't mix the two. If you need to purchase some silicone brake fluid, make sure it says "SILICONE" on the label. There are some brake fluids out there labeled DOT 5.1 or DOT 5+ which are NOT silicone based and should NOT be mixed with silicone fluid. If you search this forum for "power brake bleeder" or similar wording you will find a couple of threads describing a home made power brake bleeder based on a small garden pump-up insecticide sprayer, which make the bleeding process about 1000 times easier. Well worth the effort to build one if you intend to do a complete bleed. You can get surplus BFS for about $30/gallon, a lot better price than $10/pint at your local auto parts store.