Yeah same here, its so hard to try and put something together... After a while its hard to remember what's in each place, as the Japanese names can get a bit samey.
Sounds like you've got your head around it OK though!
In regards to carrying your bag on the train, I think the Green Class areas of the JR trains have more room in them, could be good for luggage. Perhaps someone who's actually been on them can confirm though.