Fuji isn't the easiest of places to get to. Ideally you want to stay in Gotenba around the race weekend, which can be reached by train from Tokyo. Unless you read Japanese or can be certain you get an English-speaking sat nav, I wouldn't recommend to hire a car. From Gotenba a taxi ride is the only realistic option. Fuji Speedway estimates it costs about €35:
http://www.fsw.tv/english/access/railway.html. Unless you are incredibly wealthy, don't consider a taxi from central Tokyo - it is approx 2 hours away and taxis are not cheap in Tokyo.
For VIP tickets, check out the Le Mans Spirit Club provided by WEC, which includes grid walk. I don't think they have announced the prices yet but last year it cost €550 for race day or €700 for the weekend. They usually give links on
www.fiawec.com closer to the race. You can also buy tickets there I think.
Only other tip that springs to mind is... don't expect to get an autograph from the Toyota drivers during the pit walk! The queue last year was unbelievable. Oh, and make sure you go to see the old banking while you are there.
Hope that helps.