I would bleed the MC by itself then put a brass plug in one side of the MC & hookup the other half & bleed it out then hook up the other half. A problem area that has snagged me in the past is not having the bleeder screws tightened enough & air being drawn back in. My procedure,crack bleeder screw,helper pushes pedal down 7/8 & hold, I tighten screw,have helper let up pedal.