Is this a new set up? Has it ever ran before? You can chnage teh direction of homing for the Z either by changing to home neg. in homing and limits or by changing active high/low state in config, ports and pins, motor outputs. For the Y stopping half way, try putting 2000 in the debounce in the top righ of config/general config. Also, on the program run screen, if the softlimits switch is green around the edges, click on it to disable your soft limits.
Brett
Look at this too to get your axis going in the right direction.
stick your left hand in front of you, point your thumb up, first finger ahead and second to the right, that is the +ve direction of the three axis (Thumb is z, first is y and second is X)
Also remember that it is the tool direction and not the workpiece/table. so on a mill, quill going up is Z+ve, table towards you is Y+ve and table to left is x +ve
Hood