Hi Foxy Fox, welcome to FlyerTalk!

I'm not sure what month you're planning to visit Japan, but if you're talking about next month Nov.12 to 18, then the weather in Tokyo area will be around 10-15 degrees C I think, which may be a bit cool for shorts.

I don't think there will be much problem with tattoos on your legs if you wear shorts, but if you plan to visit some temples it may be nicer to wear long trousers instead.

For prebooking the rail pass, I hope some of our train experts will be able to help you more than I can.

Enjoy your upcoming visit to Japan!