Green car and reservationtimes

Hi
We ( 2 adults) are going to Japan this March/April and I have a few questions on the Green Car tickets. Our trip is 26 days,but we will have a 21 day pass that shall be activated a few days in to our scedule as we are on buses and non-JR trains before that anyway.

We are travelling from Tokyo - Hirayu - Kyoto - Osaka - Hiroshima - Tokyo with a few daytrips thrown in.

My main concern is that I need to activate and reserve seats on the same day going from Hirayu which is not JR connected via Takayama/Nagoya on the Ltd Express and then Tokaido Shinkansen to Kyoto, so need to activate our passes and reserve seats simultaneously as we arrive in Takayma. What does your experience say, should we worry about availability? Travel day is wednesday mid-March.

My other question is luggage space. There are a few places where we'll book luggage transit services, but between bigger places I'd like to save on that and just have our luggage with us. I expect 1 medium-to-large suitcase and 1 smaller daypack-size rucksack per person. Is this feasible?

Thank you in advance
Susie