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For jeans...
Pure Blue Japan (5 mins away from teh main action)
https://www.google.co.uk/maps/place/pure+blue+japan/@35.6728149,139.7079989,16z/data=!4m2!3m1!1s0x60188ca2afdfd651:0x6fe673b91613b13eThe above 3 make a nice vague space to basically shop everywhere inbetween (shinjuku to shibuya)- lots of cool small roads (and big roads) with flagship stores and boutiquey bits all with nice gear.
Also check out Warehouse (if you're under 6ft or so) here
https://www.google.co.uk/maps/place/warehouse+denim/@35.6543278,139.6852393,14z/data=!4m5!1m2!2m1!1swarehouse+tokyo+store!3m1!1s0x60188b43f87d82e1:0xad9b89c8dd4c7e05And Hinoya if you have time
https://www.google.co.uk/maps/place/HINOYA%EF%BC%88%E3%83%92%E3%83%8E%E3%83%A4%EF%BC%89/@35.7058964,139.7727194,15z/data=!4m5!1m2!2m1!1swarehouse+tokyo+store!3m1!1s0x0000000000000000:0x6db3554cd9b3c98eSuica card (Japans Oyster card) will get you around very quick.
Blacows is ace for burgers, Tsukiji fish market for breakfast/brunch sushi.
Cheers all for the advice - Came back with some indigo's from Full Count, Evisu, Studio D'Artisan, a black pair from Momotaro, and a funky blue on blue pair from PBJ. Such great shopping over there - every shop made me try to convince myself the dream of double-denim being socially acceptable again...