If you’re worried about getting to your accommodation, I’d recommend catching the “Limousine Bus” to the Akasaka Hotel Excel Tokyo. It’s right next to Akasaka-Mitsuke Station. Akasaka-Mitsuke is flat, so you can just wheel your bags to your hotel - or if that’s too much, you can get a taxi for 510yen. The Akasaka-Mitsuke area is tiny though, so it would be pretty strange to catch a taxi to somewhere else in the neighborhood.
Also, you won’t be able to use the JR pass on the subway - but subway fares are quite low so nothing to worry about.
In most Japanese cities you usually end up doing a lot of walking. Most neighbourhoods have local buses that can get you around the neighborhood, but getting information on them can be a challenge. For example, in the Akasaka/Roppongi area, there is the “Chi Bus”. Ask the staff at the hotel. Specific places you might have issues with are Tsukiji Market (fast moving traffic/carts etc.) And the Imperial Palace (very spread out).
It’s a bit kitsch, but popular areas like Asakusa and Kyoto also have lots of people offering traditional rickshaw rides. They offer them for the experience though - they’re not a cheap way to get around.
Anyway, good luck!