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Dave,
even if the fuse is removed, the motor and recirculating ballgear (the part that transmits torque from rotation of the motor into the axial displacement of the rack bar) still move when you turn the wheel - only this time driven by your own effort rather than the electric motor. You wonder now why then you only hear the clunk with powered motor? That's because the ballgear/motor/bearing parts interface slightly different if they are driven from the opposite end.
I assume you determined the clunk isn't from the steering column/intermediate shaft as I advised earlier. It might, as you suggest, come from the motor but could also come from the recirculating ballgear. You won't be able to determine this (the S2000 steering gears' inside components can not be serviced, so you have to change the complete gear (except ECU) in either case). The root cause of your problem might be some dirt in the thread of the ballgear. There is even a chance time will make the clunk disappear but I wouldn't bet on it. Fyi, getting rid of noises and clunks in such electric gears is my daily bread, our engineers sometimes work for weeks to root-cause noise issues on a newly developed steering system.
bonne chance!
Felix
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