In reply to wjvt:
So I spent 6 months living in Omiya just outside Tokyo from December to June. Obviously climbing centres are everywhere and they're generally excellent. The place I was living was probably 99%+ Japanese, basically no tourists or ex-pats and the scene at the local wall was really welcoming and friendly.
In terms of climbing outdoors, I found a crew of ex-pats, mostly Americans, but various other nationalities as well, within my first week by joining facebook groups for local climbing scene and posting on the Reddit climbing page.
If you're working a 9 to 5 getting climbing outdoors in the week is basically impossible as even in the summer it's dark by about 7 pm. On the weekends getting to spots to go climbing is pretty easy thanks to the amazing train network. From Tokyo there's a number of decent crags within about 2 hours train, usually followed by a short walk. Be sure to look up Onsens in the area, there will often be one very close to the climbing (they're everywhere) and it's a fantastic way to relax after a day's climbing.
In general I found trad climbing quite hard to find - the Japanese tend to try and sanitise the outdoors quite a lot and this means lots of bolted routes. For example in the mountains you'll often find a chain or railing to help you up a steep rocky section. That said, there is often the odd trad line at the sport crags, and there are some good areas to visit for a weekend. The major one is Ogawayama (you probably already know this if you've done much research), but unfortunately I was there in the wrong season to check it out.
Towards the end of my trip I did manage a weekend doing an alpine rock route at Ichinokurasawa, highly recommended. This is the route I did, and I found this website to be a pretty handy resourse: https://climbjapan.blogspot.com/2009/02/route-name-south-ridge-nanryo-mount....
I also spent many weekends hiking into the mountains and staying in huts, there is generally a really good network of huts in the mountains ranging from wooden shacks to alpine huts with heating and hot meals and beer. I mostly went to the Japanese alps in Gunma and Niigata prefectures. Again, I found ex-pats with local knowledge to go with via facebook etc. Also check out OCJ (Outdoor Club Japan), they have a wierd old-school forum and an inactive facebook page, but a friend I made out there was organising a lot of trips through the site that were always good fun; unfortunately I think he's leaving Japan soon.
Sorry this post is a bit of a mess, just some scattered thoughts, will update if I think of anything else.