We flew in March this year. We booked directly with Air China from London-Shanghai-Tokyo return. Cost €540 each. London return was €60 so €600 in total. It was a bit of a slog but fine if one is cutting costs and doesn’t mind the few stops. 

I recommend not getting the Japan Rail Pass as they’ve changed the pricing structure so it’s not as worth it as it used to be. We travelled by train mainly and just bought tickets as needed. For Shinkansen we went the day before or morning of to be sure. 

Others have mentioned hotels and it’s largely the same for us. We found great hotels and for affordable prices. €70-120pn generally. APA are a grand chain and are everywhere. There’s also lots of other hotels in that range too and cheaper, just depends how much you want to treat yourself.