COBRA MASTER CYLINDER

You could do that, as far as I can tell it won't make much of a difference. I just put Cobra brakes on my GT with the factory master cylinder and booster, seems to work fine. Stops great, and pedal feel is excelent. Have you changed out your hoses? When I was researching what I wanted to do to my brakes, several brake places told me that you should do your hoses regularly. I, like everyone else on the planet I think, had never done them. Most of the cobra brake upgrades include braided hoses.

If you have a service manual for your car, (which you should), they have very good trouble shooting procedures for the brakes (at least chiltons does) that should help you figure out what part of the system is the problem.

Sounds like there is still air in the lines. Did you bleed the air out of the master cylinder before you put it on?

Did you have someone helping you or did you use a bleeder kit? You can't do it right by yourself without a kit.

Did you start with the back right side and work your way around to the front left?

Replacing the brake lines is a good idea and if there are any cracks at all in them REPLACE them. I had a line brake on me once in traffic, thank GOD for the park brake!!