I'd swing through a few shops in Tokyo first, as that way you will know how much money you have left to spend after you have bought the parts you want, and the parts that you didn't intend buying but saw them and just had to have them. It will also allow the shops time to order anything in that you need.
The last few times I've stayed in Japan I stayed at business hotels, as all I needed was a roof over my head at night. It might be a bit different with you and your missus, but they are cheap, clean, and usually close to public transport.
If you know what you want to buy, it can help if you know the prices and that they are in stock. Having it preorganised can help that way. If you want the name of a few shops then PM me. Some places are a bit further out, but with a bit of planning and an early start are definitely doable in the day. Try and see:
Nismo
Nissan Gallery
Sony store
Super Autobacs Shinonome
ASL Showroom
Toyota Megaweb
Toyota Museum & Historic Garage
If you are getting a car then go to Daikoku Futo. I'm not sure if it is current though, as the last I heard the police had been cracking down on street events.
For places a bit further out, try:
Top Secret
Tomei
JUN
Try Laurence's site for details on what is on entertainment wise: dr1ft.jp
If you are a fan of Gran Turismo, catch the train to Nagatcho station, and you can walk around the R246 track. Nagatcho station is right at the turn coming onto the main straight.