I use the Ezibleed to only get the Master Cylinder bleed, then go old school, though, on my own I find works OK on the Brakes. There is usually a residual pressure valve in the Master that aids with this, but even if there's not (as some don't), it still works as long as you have a hose going off to a jar with some fluid in it.
If you have Rubber Flexible, have you tried crimping off all of them and trying the pedal, then release them one at a time, it might show you to where there maybe some air. It may also help to bleed the brakes in this way.
If you have Single Circuit Brakes, bleeding by the 2 man method, you need to open the Rear Wheel Cylinder Nipple before pressing the pedal down.
With your rebuilt Calipers, the seals maybe dry, gripping the Piston, rather than letting them slide, so they retract much more than they normally would. Take 1 Brake Pad out at a time, pump the pedal a few times (2 or 3 is usually enough), press the Piston back in, replace the pad and continue until they are all done. This will put some fluid on the seals and allow the Pistons to slide as they should.