If I were you, I would group together
1. Tsukiji, Ginza and Marunouchi
2. Meiji Jingu, Harajuku, Shibuya and Shinjyuku
3. Asakusa/Sensoji & Imperial Palace
You have Group (1): locations on East side of Tokyo, Group (2) locations on West side of Tokyo, and Group (3) locations on East side of Tokyo.
You will minimize traveling time in the above grouping.
Like, Harajyuku/Shibuya/Shinjyku are all 1 to 2 train stops from each other, whereas if you are moving from Ginza to Shinjyku (doable, but), you have to cross town.
Depending on the timing, it may take longer than you think to cross town, I think.