This may be too late to help you, but I just relocated the factory Ford (Clarion) 6 disk changer from the center console to the rear fender shell on the driver side inside the cargo compartment. I bolted it into the little area behind the removable panel that pops out, right above where the bottle jack sits.
This install took a little creative surgery:
1. Relocated the door lock switch from the top of the fender shell to the back of the shell right below where the tonneu cover connects.
2. Had to get the longer Visteon cable to replace the one from the head unit to the center console.
3. Fabricate brackets from galvanized strapping for 3 mounting points, and had to insulate them a little to isolate vibrations.
4. Cut a rectangular hole in the top of the fender shell big enough for the changer slide door to be accessed from the top.
5. Took a little work to dress the cables uder the door thresholds, and get them zip tied into the cable trays along with the other wires already there.
The most time consuming part of this installation was probably fabricating the brackets, which was easy but took some trial and error. The harness was totally plug and play, and the only soldering I had to do was to splice in an extension to the door lock switch so I could relocate it. Cutting the hole in the top fo the fender shell was a little scary, but after I triple checked my measurements, it was no big deal.
Now I have a changer that is properly mounted and out of the way, yet still totally accessable. I like the fact that I can now stand outside the cargo area with the hatch up, and have lots of room to have my cases open when I am changing CD's. I also like that the changer is out of harms way and not flopping around, and I can still fold my seats down. BEST OF ALL, I have all that room back in the center console clamshell to collect broken pens, packs of stale gum, empty disposalbe lighters, and other such treasures.
I am planning on fabricating a cover of some kind to cover up the changer, but this is more for cosmetic reasons, and to make it less visible to potential theives, not because it needs any additional protection.
I did this for my factory changer, but you could certainly do the same for an aftermarket RF changer, or any hardwired unit with a long enough cable.
Hope this helps. Drop me a note if you want more info.
Good luck and good tunes,