So, just got back from my trip and did a lot of hunting in Tokyo, and I've got my own advice if anyone else goes and wants to find soundtracks.
1. You might find something in Akihabara, but you probably need to be lucky. I found a number of places selling soundtracks there, but finding something worthwhile didn't really happen there. I got the Contra Hardcorps and Lagrange Point Returns new at retail price there in a smaller shop on the strip, and I bought a couple used games but with it being "the place" also means it's kind of picked clean or way overpriced.
2. Tsutaya is a waste of time. I know Ryu has special releases through Tsutaya, Toranoana and Animate (both of which I popped in but didn't look around too much) but going into multiple Tsutaya stores some didn't have any music, while the bigger stores did... but it seemed like it was all rental. I found one with a bin of music they were selling (none that was vgm), and maybe they had new releases for sale but yeah total waste of time.
3. Book Off / Hard Off is awesome. So, generally I don't think you find earthshattering deals, but the prices are usually good enough to warrant picking something up. I probably went to most of the stores in Tokyo. My best shopping day was in Ikebukuro (not just at the Book Off there). I would definitely be checking in there all the time if I lived in Tokyo. The one by Hikifune station, Shibuya and Shinjuku were all also worthwhile.
4. Mandarake wasn't mentioned but is definitely worth checking out. Even moreso than the one in Akihabara, the Mandarake in Nakano takes up a lot of a mall there and covers pretty much everything. I ended up not getting it, but they had the soundtrack for Yuke! Yuke! Troublemakers for 8000 yen (I think sealed, but also a sample copy). They also had Konami GM Hits Factory II and a few other vintage albums.
5. Super Potato in Ikebukuro was better as well for soundtracks, but both have high prices on games.
6. Department stores like the aforementioned BIC Camera and Sofmap only seemed to have popular new release titles at retail price.
I feel like I only scratched the surface visiting, and wish I had had a contact out there to show me around to some places I might not discover on my own, but still I had a good time just finally getting to go.