JR pass or no JR Pass

Hi Daniel-san,
I recently asked for your help to check my itinerary and turns out, buying the JR Pass might not be the best option for me.

However, I am very confused on how I should travel without the JR Pass.

I am going to re-type my itinerary briefly.. and could you please let me know which ticket(s) should I purchase or pre-purchase (because I know that most trains can also be used by taping the suica card only, which is very convenient!)

So this is my full list:
Day 1 to Day 3: full Tokyo (3 days metro pass)

Day 4: tokyo - nagano - matsumoto

Day 5: full matsumoto

Day 6: matsumoto - narai - kyoto - shirahige jinja - kyoto

Day 7: kyoto - amanohashidate - Ine

Day 8: Ine - amanohashidate - kyoto

Day 9 to Day 11: full kyoto

———————————————— If my planning was right.. then i will only be using 2 shinkansen on this trip, which will be on:
Day 4: hokuriku shinkansen Tokyo to Nagano

Day 6: tokaido-sanyo shinkansen Nagoya to Kyoto (from matsumoto)

Is that right?
———————————————— And for the others… there are plenty of trains that have the ‘JR’ icon on google maps, such as:
1. Nagano to matsumoto: using JR Shinano/Shinonoi
2. Matsumoto to Narai: using JR Shinonoi/Shinano/Chuo Line
3. On the way to Kyoto from Matsumoto:
- Narai to Shiojiri: Chuo Line - Shiojiri to Nagano: JR Shinano

1. Kyoto to Shirahige Shrine:

2. Kyoto station to and from Katata station: Tokaido-Sanyo Line

3. Kyoto to and from Nara: using Nara Line

Was wondering if I also have to prepurchase/reserve a ticket for these? Or can I just use my IC card on the go for all of these rides?

Thank you very much beforehand, Daniel-san!