There are lots of challenges. Tokyo stations like a maze. Some stations can be confusing to navigate, specially Shinjuku station. Lots of stations have multiple exits and entries.
Eg, if you’re going to somewhere in Shinjyuku. Decide exactly which exit and which side of the exit is best.
Another challenge is pram. I believe your pram is bigger than Japanese ones. Japanese pram designed ‘light+slim’ means, there are lost of situations you have to carry your pram. Carrying your pram up and down stairs in station is so hard + 2 kids… Not every exit has elevators and escalators (or so hard to find them, sometime).
Do not travel morning rush hours!