Priming and bleeding are the same thing, if that removes any confusion. The new master cylinder will NOT be primed/bled, you have to do it yourself before installing on car. Yes, if you let it run dry, you get to start all over because once fluid is gone you are now pumping air back in again. I bleed master by putting it in a vise and filling it, then hand stroking the part with anything that will fit in the back of it. Helps to have lines attached to direct the fluid that is bled out right back into the cylinder so it does not run dry. If no lines are attached, say 3-4 inches long, there's a good chance that you will suck air back into master when you let the piston release back out, unless master is equipped with check valve/s. That part you can do with the cap off, but once unit mounted in car, better to have cap on. I have just installed master on car and bled the whole system at once before though. The fact that you bleed one line and then later it's got air in it again means you are pumping air in somewhere. If you have kept reservoir full, that means you have a bad cylinder or an air leak somewhere. Good communication is necessary with your bleeding helper, if he pumps pedal at the wrong time it just pumps more air into the system. When you bleed, do the longest line first, then go to next longest line, etc. At the first, check fluid level in master often, as you will be using a bunch until lines begin to get more full. I will bleed one line and check it. You may have to bleed the longer lines as many as 4-5 times before all air is gone. Take the time and consider while doing it, "is your life worth this extra effort?" The crud in the one line may just be really old fluid, if you get it to purge out and new clean fluid follows it, you may be fine. But, BUT, you MUST first get an airtight system that has ZERO leaks or it NEVER will pressure up. Also, unless I've missed something in the last 30 years, there is NO AIR VENT in the system. It's sealed once buttoned up. Brake fluid is hydroscopic, it sucks up water vapor from the air. A vented cap will allow water to condense in the system and start corroding things, could be the cause of that bad looking fluid. Do NOT save any fluid that has come through the system to be cheap and reuse it. It's throwaway stuff then, go buy some more. It is considered contaminated once it's been through the system.