Perscription drugs are not a problem as an earlier poster pointed out, just bring your perscription, or keep it in the original perscrption bottle.

To address you other concern such as Sudafed (btw, the same problem exists with NyQuil), my understanding is that drugs such as these are illegal in Japan as they have to high a concentration of something (don't know what). If they inspect you and these things are found, I don't know what will happen. I have been traveling to and from Japan every month for the last three years and I have never been inspected. I will not admit here, however, whether or not sudafed or NyQuil is present in my suitcase. Let just say that I don't read Japanese and if I'm sick over there, I want stuff that I know what it contains, versus going to a Japanese pharmacy and hoping that I can understand the Pharmacist!