Could be a lot of things. If the pedal is that weak though I would look at air in the lines, contaminated fluid, maybe a bad master cylinder. Leaks can suck air in and make it impossible to bleed the brakes. If the master cylinder wasn't bench bled it could do that too. Could be the wrong size master cylinder, or maybe the wrong push rod. Mismatched parts kind of thing. Does the pedal pump up at all?
Pad contamination usually means you have a good pedal, but don't stop. The hydraulic side works fine but you just don't slow down because there's no friction. Your issue sounds like a hydraulic problem.