Nice write-up.

The CD changer is not neccessary for 98-01 VWs. Blitzsafe make an adapter ($108 including overnight ship) that will enable the CD in to be used. (The HU thinks it's always playing CD 1 track 1).

I documented the wiring for my 2000 Golf. Look down the topic list, or search for it. Jetta and Beetle should be the same.

BTW, I haven't noticed any heat problems having my HU below the Empeg. The power transistors are mounted on the left side of the HU, with a heatsink on the side - most of the heat should radiate away from the Empeg, and not up. I'll keep an eye on it though.