Need help troubleshooting problem with brakes

To isolate a hydraulic problem from a mechanical one, having bench-bled the master;
remove all the wheels and remove all the calipers.
Get some HD C-clamps, and jam those pistons into the bottoms of the calipers. If the rears have a parking brake system involving the caliper, make sure it has been backed off and cannot interfere.
Now simply step on the brake pedal.
With manual brakes, the pedal should be almost instantly hard.
With a booster you will have to start the engine to evacuate the power chamber. With a booster you can expect about one inch of pedal travel before it gets hard.
If the pedal does not get hard the first thing to test is to make sure the master is properly bled, and that the pushrod depth is
correct.
Be advised that when you are clamping the pistons, this will drive fluid back up into the M/C. It can happen that the M/C overfills and you get a mess. Most brake fluids will attack your paint. Do not leave the lid off. If there is air in the system, the returning fluid can cause a geyser in the fluid that is well able to hit the underside of the hood.
After the hydraulic system has been proven to be working properly, then you can move to the mechanicals.
To add to this, and you can do this if replacing the pads, get some method lined up to first suck some fluid out of the master, so that there is room for the fluid. I actually bought a couple of big old medical syringes off ebay BUT THEY ARE GLASS. You can use them with about anything and it won't hurt them, unless you drop them.