Rockbox install
As of 2008-03-09 (r16591), support for CF cards has been added to Rockbox, no patches or workarounds are required (except when using non-SVN bootloader - see above)
So, you need to compile a new bootloader for your player using the code in SVN.
You can find info on Ipodpatcher
HERE. This should provide the info necessary to install the bootloader that you built onto your player.
Regarding hardware: Since you have an iPod Mini you should be able to simply swap out the micro-drive directly for a CF card.