my earlier post showing sources for volunteer guides still seems relevant.

500 dollars seems a normal fee for a jtb approved guide + vehicle. to bring this cost down you may want to approach the places you are particularly interested in learning about to find out if they offer tours. if they only offer tours in japanese, contact a volunteer association and enquire whether a member will be willing to help with translation.

this could put everyone in a win-win situation, your guide can focus on what is probably their main motivation to volunteer - improving their language skills - and through him/her you have access to expert, hopefully, knowledge on your interests, probably superior to that a jtb guide can provide.

as to shinagawa, as pjxf99 - /welcome to you/ - has said, shinagawa is no suburb of tokyo. and the strings makes an excellent base.

unlike other cities with just one or two centres with suburbs radiating outward, tokyo has many city centres and shinagawa is one of them, in fact, shinagawa makes an important nexus point with thousands of commuters alighting there every day. this gives it a healthy, vibrant bus until about 11:30pm. if you are a night owl, ginza or roppongi are just a 15 or 20 dollar cab ride away.