Flew there in the early 80's and not much has changed since.
Japanese CAA does NOT encourage private flying ops and really want you to fly IFR everywhere for two reasons;
1. They can be more assured that pilots use standard procedures,
2. The haze level prevalent on most days make VFR pretty iffy
Further, the controllers and local pilots are supposed to use english, but will revert to Japanese at the drop of a hat putting you well and truly out of the picture.
If you try to bring in your own aircraft then you're in for a little surprise;
You will have to have your aircraft approved prior to bringing it in and inspected after the first landfall.
In particular your engine MUST be less than five years since new/factory overhaul regardless of hours clocked. (same goes for instruments)
Only three brands of radios were approved then, these being King, Collins and ARC.
If you have any other brands like Narco etc they have to come out and be replaced by one of the approved brands.
Otherwise it's a piece of cake!