I assume/hope you can use something like this in one of the two 3,5" bays.
http://www.bol.com/nl/p/startech-com...00000014096684
Probably some creative people can come up with a 3,5" bracket that can host both USB ports and a CF card slot. Maybe the project can also include a 3D file for the 3,5" bay cover as a starting point for this, next to the backplate?