Top Secret is northeast of Tokyo Bay in Chiba. Probably about a 40 min train ride from Shibuya
https://www.google.co.jp/maps/place/....1260743?hl=en
JUN is a bit west in Iruma. 1hr train ride.
https://www.google.co.jp/maps/place/....3728161?hl=en
HKS is a bit north northwest in Saitama. 40 min train ride.
https://www.google.co.jp/maps/place/....6431828?hl=en
NISMO HQ is south in Yokohama. 1 hr train ride.
https://www.google.co.jp/maps/place/....6748381?hl=en
TOPLINE (Aragosta) is northeast of Tokyo Bay. 40 min train ride.
https://www.google.co.jp/maps/place/....0031531?hl=en
TRUST-GREDDY is quite a bit east.
https://www.google.co.jp/maps/place/...0.416664?hl=en
ARC is a bit southwest past Mt. Fuji.
https://www.google.co.jp/maps/place/....7055683?hl=en
Search Google Maps for an UPGarage ( アップガレー) around where you'll be staying. This is a used parts chain. I really wish the US had something like this.
Keep in mind, they speak very little to no English. Be courteous, respectful, and patient.