You should probably post your question on TripAdvisor forums in the Japan section. It might be hard to find a local company through DCUM alone.
FWIW, I live in Japan for two years in the 90s. Even then, pre- internet and mobile phones, everything like train signs were in English and you could pretty easily navigate if you did some research. I’m sure an American travel agent that specializes in Asia or Japan would be fine these days.
Now with Google, mobile phones and the internet being so prevalent, it is totally possible to plan and book this trip yourself, but I can understand why you’d want a travel agent, especially for Japan.
Pro tip: spend more time in Osaka, Kyoto and Nara, and less time in Tokyo.