Nice idea using the printer as a lighting box!
Just some things that came to mind:
You may keep having problems with colours if you only use the white LEDs for lighting; their spectrum sucks:
Also, if you also have a small camera with a smaller sensor, I would try that one with the aperture closed as far as it will go and compare depth of field with you big camera.
Thanks. That sounds like a very probable explanation for the excessive colour-bleeding. Maybe I will try adding more lights, maybe one of these daylight bulbs or something. Or maybe i should buy myself a proper lightbox with proper lights in it.