Surprising how many visitors don't do this and then end up wasting time and money criss-crossing Tokyo.

I'm sure you've seen that all these itineraries can be commenced by using solely the Yamanote circle line which you are well placed to get hold of from Shibuya.

Geographically speaking it might make sense to tack on Shinjuku to your Harajuku/Shibuya day (FMPOV you can easily reach Meiji Jingu walking there from Shinjuku) but heading over to Shinjuku for the evening from Ryogoku makes a lot of sense and gets you back to an area close to Shibuya so you aren't travelling for very long once you get tired (and a taxi back to the hotel is feasible also).

I still recommend a twilight visit to Azabu Juban rather than Roppongi. You can visit Roppongi MidTown or/and Roppongi Hills from Azabu Juban, the areas are neighbours and sort of compliment each other, far, far more than the foreigner ghetto cesspool that forms the main Roppongi strip. Azabu Juban is about a 25 minute walk from Roppongi but a world away otherwise. You can reach these neighbourhoods easily from Shibuya with a short bus ride.