McLaren still retain possession of the LeMans winning Ueno Clinic-sponsored GTR #01R and it is kept in a secure storage facility in England.
Reference this thread where they displayed it at ASI in 2007:
GTR 01R To be displayed at ASI ??
It was also displayed at the McLaren Technology Centre when the facility opened. There was a great photo of the three drivers - Lehto, Dalmas & Sekiya - reunited with the car that day. I'll host it later unless someone beats me to it.
I don't believe the car has ever been to Japan. The Brunei Royal Family did get McLaren to build them a replica of the car on chassis GTR #09R and that car is believed to still be in Brunei.
>8^)
ER