Thanks very much Raymond! We did actually buy the JR Pass directly from japanrailpass.net last night after we figured out that it was the only place that you could reserve seats online. It was worth paying the extra ~£48. Since we're taking our 3 year old with, it's better to spend less time trying to figure out how the tickets work in a busy station with zero Japanese.
Thanks for the tip about the Suica card. I wasn't aware that it was available in Apple Wallet. Unfortunately the Mrs has an Android phone so we'll still have to find her a physical Suica card when we get there.
Really looking forward to reading your write up. We leave on 28/04 for 3 weeks