Is the new M/C a remote-reservior type, or can you remove the cap and very the "recouperation hole" in the reservior (nearest the hose) is clear and allowing fluid return?
If the hole is clear, try unbolting your caliper and pushing the piston all the way in to the caliper, which should chase any air bubbles upward through the lines and into the M/C reservior. Make sure the brake line has a "continuous rise" with no pesky loops to trap air, and go slowly so you don't spurt brake fluid all over everything.
You might have to siphon off some fluid to avoid overfilling the M/C reservior, but if there is air in the line this process ought to push it out. You may have to repeat the process....pump the piston out to normal operating position, or slightly beyond, let things settle...tapping on the lines to encourage air bubbles to rise, then chase them up into the reservoir by pushing the piston in again. Hope this helps.