Make sure you have a JR pass for the two weeks, I used mine a freaking lot!
Don't stress about train systems, the private ones just get the cheapest ticket and pay the difference at the other end if you need to.
Also, if you are changing lines at a private station (metro etc) then make sure you dont put your ticket in an orange labeled machine (it will take it thinking you are leaving the station)
Pre book your shinkansen seats a day or two in advance so you can get a train at a decent time, however if you get on at a station at the start of the trip you can usually get a seat in a non reserved carriage.
Not all toilets in regional areas have western toilet bowls (makes an interesting event in the dunny)
Make sure you know what you want to do the day before hand, and dont be suprised if you cannot find the thing you are looking for.
People in Tokyo may say they dont speak english but a lot understand a little.
Try to work out the kanji for beed, pork, chicken, tempura, prawn etc. It helps a lot in restaurants!!!!!
Hope your single, the girls in Tokyo are f**king HAWTTTTT!
If you want to do car stuff try to get onto someone who is hooked up before you go, unless you speak the language and get a chance to stop and talk to someone who looks in the know you may be shit out of luck.
Dont be concearned with the feeling of xenophibia on the trains, Japanese dont really like having a whitie in their personal space. In restaurants they are fine serving you etc, but other than that I noticed a fair bit of racism. End of the day its their country, irony is the obsession with western culture
Tokyo for me was very different to the rest of the country, but Im not sure about Osaka.
Any other questions PM me.