As I have just re done my stereo this is all still frsh in my mind. first all after market stereos are pretty well standard in dimensions except depth. Any stereo that came from the manufacturer already installed could be a crap shoot.  As already stated depth will be your problem but you can buy spacers or make them yourself out of plastic or wood. This will allow just about any depth stereo to be put in the vanagon. running speaker new wire is suggested especially if you are replacing the original speakers. I used 18 gauge speaker wire in the front with 40 watt celestion speakers and 14 gauge wire with 200 watt 6x9's in the back. My head unit is a cheap $85.00 160watt pyramid cd radio combo that has auxilliary in and outs. It has a remote that allows you to completely shut the unit off when not in use. I will be adding a 320watt amplifier to offset power loss to the back to speakers.
    You had also mentioned that you want to hook your I-Pod to the stereo. An I-Pod should be able to run wireless direct into the stereo without any hook-up. However I cut a hole in the shifter housing(automatic) and hard wired a rca hook-up so I do not have any ugly wires hanging from the back of the stereo. This will allow me to play my electric guitar while camping or my wife driving. 
    While I was doing this I hooked up my CB in the same area. I cut a hle in the vent chamber below the stereo and there was just enough room to mount my CB between the two vents. Hope this helps Patrick 85 westy