I'm sure that you've been answered on your question re connecting the hydraulic lines to your new top motor, but if not, here goes: As has been pointed out repeatedly in the forum, the port markings on the new motors do not match the ones on the old motor. You have two choices - one is to switch the hydraulic lines to match the new port designations; the other is to connect the ports the same way as on the old motor, but you then have to reverse the electrical leads!
Now, a couple of questions: Did your dad use the bent screw driver to remove the clips, or to replace them, or both? Also, in replaciing my top after motor replacement, I couldn't get the boot that covers the top's arms to lie up properly against the bodywork. I noticed when removing/replacing the top that the screw holes for the screws attaching the "hoop" to the body are elongated, except for the center hole. Is there a sequence in driviing the screws in the holes to either side of the center hole that will cause the hoop and its seal to lie up better?