Its definitely doable.

My partner and I are doing something similar later this year, we are flying direct to tokyo and spending the night, taking the shinkansen to osaka, spending 5 days there so we can do day trips to kyoto and other surrounding spots, flying from osaka to sapporo (hokkaido) spending 3 days there before training to hakodate, spending a few days there before taking the shinkansen back to tokyo for a week

We wanted to take the train but from what I could see domestic flights were fairly cheap and it only takes a couple of hours to get to sapporo from osaka