as u stay there, ur jap can really improve. 
one thing, most signs in tokyo come with english, though not all.
if u're in tokyo, u're pretty safe with chinese knowledge (to
recognise kanji), katakana and hiragana syllable tables, some
common phrases, and u can use english or point to the menu.
train system is indeed confusing. train stations are structured in
this way, in one axis are all the thin platforms, as narrow as
bishan or more but longer, packing more ppl. at different parts of
platforms are the escalators or staircases to the different exits
of the station, either overhead or underneath. to get from one exit
to another (while inside), u have to squeeze thru the platforms. no
joke. exiting at the wrong exit, u might have a difficult time
navigating through from outside, once in a while u might want to
tap ur card in (if u use card instead of manual tickets) and head
to another exit's office, hand over ur card apologetically and the
staff will know what to do. 
here's a pretty recent thread for u to read.
http://sgforums.com/?action=thread_display&thread_id=246077
but imptly i must noe how many nights u're staying and if u're
intending to head out of tokyo. 
