If Smashboards wasn't down, I'd get the link to GCT Edit.
GCT Edit isn't exactly the best thing to use, it's very glitchy and screws up with codes it doesn't recognize.
Instead, the easiest thing to do is find out what codes are on each .GCT (if you already know, then good, that's one step easier), and make a text file the codes from both .GCT's, and then open that .txt in Code Manager and check everything off and export as .GCT.