I am at a point on my CJ5 Build where I need to worry about the brakes
Here's what I got
Front: D-44 converted to disk brakes
Rear: 14-Bolt converted to disk brakes

**What Type of master cylinder should I use?
**What other parts besides the MC and Brake Lines am I going to have to buy?

Any other useful info would be greatly appreciated.

You can see the build here
http://www.4x4himphoenix.org/1975%20CJ5.htm

Cool rig.
MC depends on the size of pistons in the calipers, and type/size of brake booster you have. So what calipers and booster are you running?
You may also need an adjustable proportioning valve to adjust the braking bias between the front and rear brakes.