1. Can anyone tell me where I can find (if any) the pre-run cable in the trunk for a cd changer?

2. If my car is not equipped with a pre-run cable does anyone know where I can find a stock CD Player for a 2000 Bonneville SE?

Try the junkyard. You can find a stock one for pretty reasonable.

umm.. I dont know what the junkyard would have to do with anything. But the 2000+ bonnes are not prewired for CD changers if they are not euqipped form the factory with one.
you can always add a FM modulated unit and still keep the factory headunit

FM Modulators are crap. Just go with an aftermarket CD Changer

I have had experience with 2 types of FM Modulators...

The first was the Radio Shack special, the transmitter. Which I agree was absolute crap.

However the Alpine changer I had in my Firebird came with a different kind of FM modulator. It wired in between the antenna and the deck. Worked quite well for me. Maybe with a "proper" "high performace" audio system (ie one for a competition) they are pointless, but it served my purpose just fine.