Great question!
I would recommend editing it to either be system-agnostic using stand-in stats for similar D100 systems (like Five Million Worlds). Then once you get approval from TKG, editing your submission with the Mothership license/compatibility mark.
And if you want someone to look over your submission, feel free to hop into the Sci-Fi Collective Server. We have some other people (*cough* me *cough*) doing some last-minute work, and can probably make time to help you out with anything else.