Hey there, I just got back from japan today so I can offer some advice with a few of those places. I wanted to experience more of the car scene but ran out of time. I would highly recommend the nismo factory in yokohama. opening hours are wed-sunday 10am-5pm free entry. parts are very pricey though but still an amazing experience and just under an hour by train from Tokyo train station. I checked out one upgarage in Tokyo but it wasn't that great. It was the one in minamitanaka, nerima, tokyo. it had 2 levels...the first with lots of good quality super cheap rims and the second floor with mainly head units, exhaust systems and coilovers, but not a lot of options for skylines. It might be worth checking out some other up garages though. I also went to an Autobacs in Osaka. It was the deiribashiten store and only a very short trip from Osaka train station. Not worth going to in my opinion, they only had car cleaning products and focused on interior parts and a decent selection of rims. The super Autobacs would be worth checking out though. Hope this helps you