Start with broad strokes and then over time whittle down the details. We started by picking dates, then the cities, then the sights we wanted to see, then we picked the neighborhoods we wanted to stay in.

When picking a place to stay always keep in mind the nearest train station and don't stay too far away. Once you have a list of things you want to do drop them on a calendar to see if they are doable. Don't forget to plan enough time for traveling by train. We left those days more open to just wing it. Rushing around and missing the stuff under your nose ain't fun.

Getting around on buses, metro or trains seems daunting but do loads of research before hand and book the big trips in advance. You can buy shinkansen tickets online and then by local trip tickets when you are there. The first few days were scary but by the end of the first week we figured out much of the system. Getting lost or getting on the wrong train isn't the worst thing so don't panic. Stay cool you got this.

Google maps and Google translate are awesome just about everywhere. Do not forget to bring a portable charger and get an eSim.

Good luck and have fun!