I don’t recommend driving as I recall remarkably few signs are in English especially once you get off the beaten track. And the trains are great. Do stay at a ryokan - we did twice, though I admit that the arrival and departures were facilitated by English speaking professor friends of dh’s who helped us understand what the routine was going to be. That way when we got an unintelligible call at a particular hour we were able to guess it was bath time or dinner time.
We did not spend enough time in Kyoto and I believe you have to reserve a time to see the beautiful zen gardens there.
Instead of going to Disneyland why don’t you go to the Japanese version? Our kids favorite thing in Japan (8 and 12 at the time) was Edo Wonderland - which is kind of like a Renaissance Faire. Lots of acting in the street which we could understand, mazes, craft demonstration, and the “house of illusions” which all of us loved. http://www.japan-guide.com/e/e3879.html