The 03/04 tops are not easy to find, but with more people converting their cars to track cars they are coming up more often. I found my 04 OEM top on Ebay for $900 this Spring and it was nearly perfect. Then I was able to sell my 02 top with a fairly new/replaced plastic window for $550, so for me it cost $350 (plus $100 shipping) to make the swap. When I had my last plastic window replaced it cost $600, so the upgrade was a pretty easy decision.
The glass window is definitely smaller. I think it looks better/updated from the outside, and since the top is usually down it doesn't affect my view driving.
As for the chop, I didn't always do it because when it was warm enough the window would fold nicely. When it was cooler (I live in MN) I always did it because I still remember the sound of my original plastic window cracking.