Hmmm. This is the classic: Nothing is wrong but something is. Happens to me all the time, unfortunately.
First, I would say it sounds like you have air in your lines "Only way to stop is to pump the pedal hard". I would also concentrate on your front disc brakes, since they provide most of the stopping power. If they worked the car would absolutely stop.
Some other questions and thoughts:
- In know, a very basic question: Are your bleeder fittings at the top of the calipers? They must be at the highest point. Some people have mounted the calipers on the wrong sides and that leaves air in them.
- What is the bore of your original master cylinder vs. you new one? They should be the same. An incorrect bore size could cause issues.
- You say your brake warning light is on. This switch is in your proportioning valve, so that is telling you something is wrong there. Either it is still plugged, or has air in it, etc. On my 70 Road Runner, I disassembled it carefully, cleaned it, and then put it back together. It really is not that hard, so that might be something to try.
- Are your brake hoses new? Some hoses collapse on the inside. You can't see it, but they then inhibit fluid moving through them.
And, please be super careful with brake fluid. Be SURE you protect your paint; it will eat your new paint very quickly: Ask me how I know (I screwed up the paint on my 70 Limelight Road Runner TWICE due to issues. Grrrrr.....)
Maybe a picture or two of one of your calipers will help as well.
Hope some of this helps,
Hawk