Get a subway map and Pass and travel out of the core downtown area. Tokyo is not one big city but rather a conglomeration of many smaller cities, many of which have their own character and personality. You are unlikely to find those by just randomly walking or riding around. Did you not think to bring a guide book or other information for a two week stay?? If not, look on-line for help. Japan Guide - http://www.japan-guide.com/ - is one, there are many others. Just get out of Shinagawa, which is a pretty boring part of Tokyo.

It is possible your friend is still suffering from jet-lag. If not handled at once, it can hang on for a week or more. That would explain the late mornings and early evenings. He needs to get up in the morning - even if it is hard - and get out in the sunlight.

Why did you guys even come to Japan? It sounds like you had no plan. With two weeks, you could have gotten out of Tokyo and seen large sections of the rest of the country. With a week left, you can still get out of the city and see Kanagawa, Nikko, Matsumoto (in the mountains,) the coastal areas and much more. You need to get out and enjoy your visit - with your friend or without.