Estimating transportation cost?

I shortened my trip down to less cities to try and get the cost a little better but I feel it’s kind of hard to know the accurate cost as well as if there might be a better way.

I have Tokyo to Kyoto with a day trip to Himeji, then to takayama and back to Tokyo with another day trip maybe to kawaguchiko or Nikko. (Although I’m also considering maybe if I just started in Kyoto that would be part of the flight instead)

I’ve used the JR pass calculator and got that cost (does not pay off) and then I also tried to look each up separately by myself.

I have for two people about $900 total. Looks like shinkansen is usually 16,000 each. Although for Kyoto to takayama I picked bus which maybe might not be the best? I figured even if it’s longer it’s scenic, but not sure if taking a bus is more confusing

I want to take a fast train at least once but it doesn’t have to be for the full trip if it can be cheaper but still good. I think the only limited express train I have (what I am assuming is more like a regular train in the us?) is for the Tokyo day trip.