100 Stay, a couple of stops down from Shinjuku is good. A lively, non-posh area close to Koreatown, with lots of good, cheap eats, excellent transport.
If you're not fussed about cherry blossom or maple leaves, late September, early October are good.
All transport is announced in both Englsh and Japanese, and is flashed up ditto on screens.
DH and I are in Japan on our second visit, have little to no Japanese, but managed perfectly well, with konnichi-wa, arigato and bowing. Bowing is good, seriously, as is enthusiasm for the food, eating with chopsticks, and adoring the Shinkansen.
OP, if you're travelling about, investigate the Japan Rail pass, which can only be bought outside Japan, but will save you a fortune.