I recently did this on my '01:
It's not a simple task, but doable if you are handy. I linked to some instructions on ehow that are adequate, but could use a little more fleshing out. They also ignore replacing the rear window which is of particular interest to you.
If you have a decent selection of tools already, the main thing you will need is a stapler and various length staples. I got one from Harbor Freight that did just fine for about $20.
You can do the rear window without doing the main top, but I'd do both if it is the original top since you will have the main piece 80% removed anyways.
I bought an "EZ-On" top through Amazon.com. Quality seemed a little better than the OEM top I removed. If I had a black top, I would have gotten a kit from http://www.latemodelrestoration.com/
(Site sponsor) that comes with both parts of the top and new pads, but they didn't have the kit in "Parchment" and the cost is higher as separate pieces.
One of the more time consuming parts of the job is pulling staples. I would guess removing the top yourself and having a shop install would save you some cash. Although I could see a shop wanting to see and mark where the old top was installed. Be sure to keep fasteners organized (I like Ziploc freezer bags that you can write on) to make it easier to reinstall.
Good luck, whichever route you take.