tlrskunk

Pad compound makes a huge difference in stopping power.
All you have addressed with your statement is the fluid dynamics part of Braking. Add sh*t pads and it still won't stop.
Decreasing Master Cylinder, while increasing piston size can cause you to run out of fluid movement if you aren't careful as well. Use caution. (This is an extreme Scenario)

Kubs

Joel is correct. Decreasing MC size will increase the stopping power WITH THE SAME AMOUNT OF EFFORT. The trade off is you will have a much longer travel though. You have to balance the MC bore size and total piston area of the calipers to the amount of travel and effort you want.

I went from the stock 7/8" MC to a 1" MC because the stock travel was too far for me. The brake pedal would end up below the throttle pedal making it more difficult for me to heal/toe downshift. By changing to a 1" bore, the car stops the same but the pedal doesnt travel as far. It also requires more effort to push to get the stopping power back (not a huge difference for me, but a 90 year old lady probably would have trouble driving my car compared to a Cruze). The other thing that changed is my modularity of the pedal. Because of the increased fluid displacement it takes less pedal travel to modulate the brakes. Again, not a huge difference in my case but noticeable.

96CollectorSport

Wow a couple of you guys are pretty easy to attack someone for trying to be helpful - I was simply pointing out the misconception that a larger master cylinder will give you more stopping power. Years ago I too thought a larger master cylinder would increase stopping power, until someone explained to me how hydraulics work - I was grateful for them sharing that information.

When playing with master cylinders it's important to find the balance that Kubs mentions - too small of a master cylinder and you may run into issues with low pedal height - but the opposite is also true - too large of a master cylinder and you will barely have to move the pedal making the brake pedal more like an on/off switch with poor modulation.
I have a brake force calculator that I use to compare how different components work together, this gives me a pretty good idea on how a system will behave before it's installed. This has helped me and my customers build some really good brake systems with good balance, heat control and increased pad and rotor life.

This is an impressive build, well done! Once done it will be one bad *** C4 for sure!