New sunroof motor will not reprogram!

Any helpful direction would be appreciated. I ended up replacing both sunroof and sunshade motors because of a clogged sunroof drain, but I cannot get the sunroof motor to reprogram. I manually closed the sunroof by pushing the cables with a screwdriver and putting pressure on the sunroof. Before I realized I could take the circuitboard cover off of the motor and put vice grips on the shaft and turn the sunroof that way. Unfortunately when I did that, I was only lowering one side of the sunroof, so one side was almost all the way down, and the other side was almost all the way up. So to correct the problem of it being uneven, I put the sunroof in full tilt position by moving the cables and reinstalled the old motor and use the vice grips on the shaft to lower it to close position. But the front right corner of the sunroof stuck up further than the left the part that is not supposed to tilt or move very much. But I was able to move the sunroof with the sunroof switch back-and-forth. It would go to for open position and full tilt position, but when it would go to fully closed position, it is about a quarter of an inch too low. I can use the tilt switch to raise the sunroof up to where it should be in closed position and have tried reprogramming the motor but the motor will not reprogram. I purchased both motors off of Amazon. So now I have it. Duct taped until I can figure out what to do. Any suggestions?