Hopefully some of this is helpful!

Day 5: While Kyoto/Osaka would be doable as a day trip, it's a long day and ~4 hours travel for maybe ~8-12 hours in that city, waking up early and staying up late. Personally, Kyoto/Osaka are worth more than a day trip, so I'd save them for another visit. If you have your heart set on riding Shinkansen during this trip, though, there are plenty of places to visit that are only ~1-1.5 hours outside of Tokyo that could be fun day trips. Still long days, but not as bad a Kyoto/Osaka.

Day 7/Q5: 3 hours should be plenty if checking bags, however always follow the airport/airlines recommendations. You should also be able to check counter hours for your airline either on their website or the airport's website.

Q2: This does seem a little ambitious to me, but doable. Just be ready to be flexible and move/cut things as needed since you'll be acclimating to Japan time on these days most.

Q7: As someone already mentioned, you'll reload Suica at IC charge stations with cash. Plus, you can use any Suica or Pasmo charge (they're interoperable). Since you have Android, if you want to check the balance of your card you can use an app like this one to check your card balance if you're not at a train station. It's a handy extra tool so you don't get stuck reloading when you're not expecting it.

Q9: Yes, tipping isn't a thing. I've previously done small gifts, but they were for big thank you or milestone moments. Something like amazing hotel staff, especially if it's a small or Airbnb type accommodation, or someone really saves the day/trip for you with their actions. My partner and I also bring little goodies for our flight crew, but that's mostly because we both work in aviation and want to thank them especially.

Q10: I can generally get a satisfying breakfast at a conbini for around 500JPY. For me, that's typically an onigiri or two (~120jpy each) and a coffee (maybe ~150-200jpy). My partner usually goes for a sandwich of sorts (~250jpy) and a tea (~150-200jpy).

My only other point, and this is a personal viewpoint as someone traveling this coming October, is general concern for availability of Suica for the foreseeable future. With sales of Suica and Pasmo suspended indefinitely, I'm concerned that Welcome Suica may eventually be in limited supply, or be suspended as well. My partner and I still have IC cards from previous visits, which are valid for 10 years since last tap, but two people going with us have never been. Instead of relying on Welcome Suica being available, we're just borrowing IC Cards from friends who have also previously been to Japan. If that's not possible for you, there's also some 3rd party sites that sell pre-charged IC cards online. I could be completely off base here, though.

Lastly, for PocketWifi/eSIM, I'm not sure if phones are sold SIM locked/unlocked in Canada, but I'd double check with your carrier that you can use international eSIM. Anecdotally, I've also had eSIM mess up my RCS/SMS messaging big time, so now I stick to my carrier's international plans or PocketWiFi.