Can I take a medium-sized suitcase on the Azusa Express from Matsumoto to Tokyo (and on trains in general)

Hey Team,

Organising our first trip to Japan as a family of 4 in late September/early October.

We generally travel pretty light, and between the four of us (kids 10 and 12) we will have one medium sized suitcase plus 2 small everyday backpacks (phone, water bottle…).

From everything I read online you seem to be come a mortal enemy by taking a suitcase on a train. I do understand that if you are lugging around a massive suitcase big enough to fit a child in will be a PITA for everyone else on the train as there is no space for these.

BUT can I take a medium sized one? Where can I store it, are there overhead racks or an open area by the door?

We are taking the train from Kyoto to Takayama.
We are staying at an AirBnB so if we had to send the bag, we'd do so from a konbini.

From Takayama we're renting a car for a few days to tikki tour through the Alps (Shirakawago, Hida Furukawa, waterfalls, Nakasendo Trail…) and then end in Matsumoto, where we'll return the car and hop on a train to Tokyo.

This is the train ride I'm thinking about the most. We will only be in Matsumoto for a quick lunch and look round the castle, so can't really send a bag from there.

We are staying in Magome for 2 nights, but there is no konbini, so would have to drive to Nakatsugawa and send it from there I imagine.

We are staying at an AirBnB in Tokyo (Shinjuku area). Our train from Matsumoto will arrive at Shinjuku Station, and from there it's I think only one or two stops to where our AirBnB is.

By the time we arrive we will have driven about 2.5 hours from Magome to Matsumoto, checked out the castle and then a 3hr train ride to arrive at a massive train station – so I'd rather just have my bag with me and go straight to the AirBnB.

So long story short – will we be OK to take our suitcase on the train?

Sidenote: Will we have to reserve the tickets from Matsumoto to Tokyo online in advance? We're looking at an early afternoon departure on a Monday early October, 2nd class, but would like to sit together. Or at least 2 and 2.

Thank you!