I upgraded from the D3 to the F90BT and my CDX-P680 isnt working now. I know there is not a direct source for a CD Changer, but is there any way to make a changer work on one of the external inpurt or something???

You could use an external add-on CD changer that has an external display that is used to control the CD changer that plays through the auxiliary input.

My question is why? With SD cards, USB drive and iPods, there's really no reason to use a CD player (unless you're worried about sound quality, in which case you wouldn't have selected a Pioneer headunit).