CT has a prescription for Adderall (methamphetamine), which is illegal in Japan, and has recently been hired to work on a U.S. base here.
"My plan as of now is to leave my meds at home and try to get a new prescription once I'm on the military base, which is considered sovereign U.S. territory. I know that I won't have a problem there since I'm already in the military medical database, but the dosage available at the military pharmacy is much weaker than my current prescription, if it's in stock at all when I arrive.
"Since Adderall is a narcotic, would the Narcotics Control Department even issue me a special certificate given that it's illegal? Or can I get an exception since I'm just 'passing through' to a military base?"
We contacted the Narcotics Control Department and they said there isn't any way to bring methamphetamine into Japan, even if you are just transiting through to the base. They also suggested trying to get a prescription for a similar type of medication here in Japan, although in your situation the best way to go is probably to acquire a new prescription on base.