Most Travel Agents work with corporate organisations such as these linked below and don’t themselves tailor the trips. It is worth noting that the travel landscape has changed so drastically that only firmly established corporate organisations might be able to offer dependable tours at the moment.

TNK Land Package | Tonichi Travel Japan
https://www.japan-san.net
Tours to Japan from operator Gold Tour Japan
https://travelio.jp/japan_en/
https://www.jtbgmt.com/en/leisure/grouptours/

Finding what you are asking for that includes dinner bookings might be more elusive. There are “fixers” (when famous chefs visit Japan it’s usually a fixer who decides and arranges where they will eat and popularise), but you’ll probably be better off relying on your hotel’s concierge. One of the the more premium tours (like those provided by Tonichi Travel Service; the Japan-coachman.com link) will have hotels of a high enough calibre in their itineraries that would provide this service.