Just went thru this after changing calipers. Make sure your rear drums are adjusted up properly. Does your new M/C have a built-in proportioning valve ? If not you may need to add one. If your M/C is mounted below floorboards you should have a residual pressure valve on system. ( Check out Wilwood website for info. ) As Jock says, there is some adjustment on the piston rod between the booster and M/C - make sure you still have clearance on this or your brakes will seize up as pressure is not fully released each time you release the pedal.

1940 Chevy KC 1/2-Ton
In the Stovebolt Gallery