I'm currently running s14 brakes on my 86 and am going back to a standard ae86 brake.
Do I need to change my brake master to accomodate or should work fine?
The stock master will work. It may be a little undersized and give you a slightly spongy feeling pedal. If you don't like it you can fit a larger bore master, there are plenty of options (assuming it's an ADM AE86): Corona, Pajero, R32, etc...
Probably the most important part is making sure you have reasonable brake bias once everything is installed.