Yeah, any time you open the system, you really should bleed it out, again. It doesn't take even a single air bubble to cause problems, and a single line broken open to make an air bubble. Sp yeah, when you opened the system to replace the master cylinder, when you replaced the lines, etc etc etc. That's why you should try and do everything at one shot, if possible. Saves a lot of brake fluid
Good luck, and let us know how things work out for you
Pat☺