Japan Transportation

Hi everyone, in November 2025 I am travelling to Japan for the first time. I’ve booked my flights & accomodation so my itinerary is locked in, but I’m really struggling with understanding how transportation works. Specially how to get from place to place, whether I need to pre book, and the multiple stops / transfers make me very nervous. I don’t really understand the difference between Shinkansens, trains, bullet trains, etc. I’m looking for advice / tips on how to get from place to place easily and quickly. My itinerary and some commentary is below:

• Arrive Tokyo NRT 5pm - travel straight to Asakusa (1 night) • Asakusa - Nikko (3 nights) • Nikko - Omiya (1 night) • Omiya - Takayama (4 nights) • Takayama - Gero (1 night) • Gero - Nakatsugawa (3 nights) • Nakatsugawa - Tokyo (Shibuya) (4 nights) • Tokyo Shibuya - NRT Airport

I’m worried my trip doesn’t make sense from a transportation / logistics perspective as it’s a bit different. Can anyone put my mind at ease?