I was mainly hunting for pedals and read that Ochanomizu area was not the best for those so I skipped it completely. I'm going to Japan again in August so might check the area then.
Digimart.net makes it a lot easier to find what store has what, so you don't necessarily need to even visit or go through a bunch of websites. If you haven't already, I recommend you try using it to find used lefty LP style guitars.
I mentioned them earlier, but the Hard Off stores in Akihabara might be worth a visit too. There's a few pretty close together so it doesn't take long to go through them. Their prices at least for pedals were cheaper than what you find in music stores. The guitars on the wall ranged to surprisingly high end for this sort of store, there was a Custom Shop Fender in one of the display cases for example, and a beautiful Momose Tele for around 2000€ hanging on the rack. I would have bought that if I hadn't gotten a Tele last year.