Hello. I am not sure about the copper wire, but it is most probably for the radio. I replaced my plastic window 2 months ago for $300 with labor. It was a DOT approved plastic window. I think they did a pretty good job. No leaks so far. I did not have a copper wire in my 00 Box.
Here is a picture of my new plastic window.
Picture is too large, so just go to links.
IMG_4190 | Flickr - Photo Sharing!
All sizes | IMG_4166 | Flickr - Photo Sharing!
Incase they forget to tell you. Do not wash the car or use the top for the first 24 hours and let it sit in the sun. At the same time, make sure the electronic top does move when you hit the switch so you know they installed it right.