My 97 window is all scratched up too. Don't replace just the window as you can get a replacement top for less than $400 on Ebay.
Since you live in the frozen north, you won't be using the car much in winter anyway, so few people will ever see those "stars" in your back window. Just keep the top down at all times like I do down here in Houston, or what we call "Sauna City".
Went to college in St. Paul...I pity anyone who lives in MN in the winter. Summers are gorgeous and the best Boxster weather on the planet, but the other ten months out of the year are brutal!