What is going to happen when I remove the master cylinder?

in a 66 A the push rod is no problem.I have done this swap more times than I can count and never had any issue with the push rod. If you are going to disc brakes from drum you had better make sure the master you are going to use is for disc brakes. They are different for disc and drum. You will also need a proportioning valve and the correct metering block because now you are adding seperate lines to feed the front and rear brakes .