I sure would think that using Ghost with a IDE/CF reader would work just fine; The smart thing you did was to get an IDE reader as that allows the CF to be read in native mode just like a hard drive.
GCT's in a POS situation? WOW! As that sounds creative, I would believe there would be a better solution as the hardware support is a little weak.
Getting back on subject however, I would stand to believe that Ghost would be able to image the drive and allow you to duplicate the CF; I would assume that there is a flavor of Linix involved but I believe you are on the right path using an IDE CF drive instead of USB, Ghost should allow you to create an image of the drive and save it as a file to later duplicate to another drive, Ghost works on a drive image and really shuold care to much about the partitions as much as it duplicate the drive by bit by bit.
Get your IDE drive going and post back your results.
my email link in my profile should work, drop me a line if you like, I am not interested in money but I have worked on mod'ing the GCT's with hard drives and such so I should be able to offer you some advice.