Pads should be very close to the rotor.There is an adjustment screw/bolt at the master cylinder- have you tried to adjust the bolt longer?,not enough throw into the plunger makes a huge difference.That last little bit of push was critical for me to get them to work after the master cylinder got some wear and tear on it. I replaced my master cylinder twice for exactly the same reason-wouldn't lock up brakes after a short while and then wouldn't bleed to get good pressure. I finally got a motorcyle master cylinder and haven't had any more issues.
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