Hello,
We've discussed the glass rear window. Check the forum, but the conclusion was that it wasn't really feasible. The thinking is that it would take around 15k to retrofit the glass rear window.
As for the price, I just bought a 2000 boxster (not S) with 30k miles. Mine didn't have as many options. No heated seats, and no CD player, but leather, and the convertible top was absolutely perfect. I paid 9k less than what you're thinking of paying before the extra 2k for the 'certified'
You'll have to make your own choices of course.
Good luck,
JBG