Were you ever able to figure this out?
To do a full race conversion so the game will accept the race flips, you will need the following:
Photoshop or equivalent for creating the Cardassian emblems, artwork and rank insignia. All artwork must be saved as bitmaps to the game.
a Q3 editor to allow you to view and edit the Borg and Cardassian artwork and flip their assigned slots. From here, you can also change weapon icons and hud items.
Artifex map editor for Starfleet Command. Once you have flipped the assigned arrangements in ALL the relevant Assets and MetaAssets file folders*, the map will need to reflect your changes, otherwise the game engine gets goofy when attempting to execute the changes. This can be the reason you can't generate stations (because they have to be added to the map), refit at presumed friendly planets and stations and why you get attacked by your own AI.
The above programs are necessary for a true race swap and to avoid disappointing game play.
*As far as flipping the races, the change must be done in each file that lists both the Borg and Cardassians. This includes the line item references in the strings and aaSrings found in the Strings sub-folder for Assets.