OP -- Nearly all of your assumptions about travel in Japan are off base -- trains can handle your luggage easily, the stations all have easy to understand english (especially after the Olypmics) -- and Shinagawa station (my old station) is by far the easiest station in Tokyo to connect via... If connecting at Shinagawa worries you trust me taxis are plentiful and easy -- for $30 you will arrive ant Haneda with no drama.... The train - as so many have correctly have pointed out -- is very easy.... Honestly -- way more can go wrong with a flight than the train -- enjoy your tour and take the train -- and let the stress go....