2. Nismo is in Omorikaigan, Yamanote line to Shinagawa. Easy to do from Tokyo is your staying Shinjuku etc. Top Secret is a 30 minute train ride to Chiba and a taxi to the shop. There's also a Crystal down is Chiba. Catch the monorail and get off at the stadium.
3. The Lonely Planet wont have any info on motorsports but it is useful. Akihabara, Shibuya, Ginza...all worth visiting in Tokyo
4. I use trip advisor...always a few deals to be had
5. I wouldn't, the public transport system is excellent and part of the experience. If you can read Kanji and speak Japanese...no problem. This is the link to a pdf of the JR East. Put it in one of those silicon map cases and keep it with you. The further you get away from the main lines the less English is used to describe the train or station. On the platform signs red means express, green for limited express and white means local or all stops. Always stick to the left of the escalators...right side is for walking, left side is for sleeping lol. Phone hire is good idea if you have different tastes and want to look at different things.
Most of this has been covered...have a search and enjoy the experience