what line go's where?

... I'd take it off the car and bench bleed again ...
Agree, except I always "bench bleed" w/ MC on the car, even a new MC. I don't like the flimsy plastic press-in bleed adapters that come w/ some MC's. Better are ones that screw in. I have some made from old 3/16" metal tube w/ a stub of clear plastic hose to see air bubbles. Secure the hose well at the reservoir. You don't want it flopping loose and spraying brake fluid all under-hood, since glycol is a great paint remover and why most cars we inherit have rust all under the MC from leaks. You may have to pump 50 times to flush out all bubbles.