The BRAKE light coming on means you are either low on fluid, your parking brake switch is busted, or on a diesel engine a vacuum issue (may be the sensor or the vac pump). You MUST resolve this issue before continuing. ABS light will be triggered and the system disabled by the red BRAKE light. You need to make sure the master cylinder has been properly bled. If it has had air in it, they can be hard to bleed. Fords official procedure for bleeding the brake system with RABS:
Hydraulic System Bleeding
When any part of the hydraulic system has been disconnected for repair or replacement, air may get into the lines and cause spongy pedal action. This requires the bleeding of the hydraulic system after it has been properly connected to be sure all air is expelled from the brake cylinders and lines. The hydraulic system can be bled with pressure bleeding equipment such as Rotunda Brake Bleeder model 104-00064 or equivalent.
Bleed one brake cylinder at a time. On E-150-250-350, F-150-250-350 and Bronco vehicles, start the bleeding at the right rear brake wheel cylinder and then at the left rear wheel brake cylinder. After completing, proceed to the Rear Anti-lock Brake (RABS) Valve. Then proceed to bleed the front brakes, starting with the right front brake, and finish bleeding on the left front brake. On F-Super Duty vehicles, start the bleeding at the right rear brake, then the left rear brake. After completing, proceed to bleed the right front brake and then the left front brake. Keep the master cylinder reservoir filled with the specified Ford Heavy Duty Brake Fluid C6AZ-19542-AA or -BA (ESA-M6C25-A) or equivalent. Never use brake fluid that has been drained from the system.