You can find the navigation cd's all day long on Ebay. Just do a search for "mercedes navigation cd" and you'll have several auctions come up.
I also have a 2000 S500 and I'm moving forward with replacing the navigation system. I've done quite a bit of research and I've opted to go with a Kenwood DNX-7100 GPS unit. I'm also adding the bluetooth, Sirius, and Ipod controls. The biggest obsticle is what to do with the wood bezel that surrounds the navigation unit. I went to 3 or 4 custom shops and they all told me that the best they could do is make a custom bezel but it would be the same vinyl as the dash. Finally I found a shop that will do a wood bezel that will match the rest of the trim. It's a little more expensive but vinyl is not an option for me.
The second obsticle is what to do with the speakers, amp, and cd changer. The factory navigation is connected to the amp using fiber optics. Once I change out the head unit, the amp, as well as the cd changer in the trunk can no longer be used. Since the factory head unit is designed for 4 ohms, it could easily overheat since the Bose speakers are 2 ohms. For this reason, I'll be adding an Alpine amp so I can continue to use the Bose speakers at 2 ohms.
To make a long story short, in a few weeks I'll have a new GPS unit, new amp, bluetooth, Ipod, and Sirius. The entire package including parts and installation will cost about $2400. My 2000 S500 only has 24,000 miles on it so to me it's well worth the investment.
Here is a picture of what someone else had done with a Pioneer unit and I'm anticipating similar results.
Hope some of this information helps.