power window problem(clunking noise)

[GMCANYON]

I have a 2000 sunfire. I have tested the switch and motor and it was the motor that wore out. It was only going up a little bit and cutting out. I purchased a brand new motor from the dealer and did the following:
- removed door panel
- taped window up
- disconnected window from regulator
- removed the entire assembly from the door
- marked where the old motor matched up on the regulator
- drilled out the rivets and attached the new motor
- put the motor and regulator back in place
Now when the motor goes up its fine when it is almost all the way down it will not go completely down and makes a loud clunking noise. Can the motor or regulator be adjusted. How do I fix this. I can't find a forum on this problem. The car has 160 000kms + the dealer is not an option to repair this.

Thanks
DM