Technically anything non ADR compliant on the car has to be replaced by a compliant part and the aftermarket part that was removed from the car has to be destroyed (not sold) by the compliancer.
Whether or not that happens in reality is another matter.
If I were you, make sure whoever is handling your importation does an inspection in Japan before the car leaves, and if possible give you an itemised list of aftermarket parts on it. Then when it gets through compliance, if the compliancer wants to run the risk, see if they'll give you those parts back.