When you replace a regulator you should cycle the window several times to set the limit switchs. If the window is not tight in the regulator the limit switches will stop the window early. Replace the window clip 51 33 8 254 781 and be sure the window is not moving around in the regulator.

The other problems are probably related to disconnected wires in the door. Also look at the door check switch, sounds like that is either not engaging or disconnected.

Oh and pick up some door panel clips 51 41 8 224 781 I'll bet the ones your using are beat.