Osaka > Kyoto - Fushimi Inari Taisha > Nishiki Market > Arashiyama > Osaka
mate, you spend quite a bit of time in each of these places and it takes a fair amount of travelling to get to each point. You can do Fushimi Inari and Nishiki together. Arashiyama is most likely out of the question.
You are going to see crowds at Tsukiji, the inner wholesale market has moved iirc but the outer market is what most ppl go there for anyway
Roppongi is nice but it is a little hard, there is Mori tower which has an observation deck. There is a shrine that is a little off the track there and got nightlife which I am not too into
