I’ve now had a chance to look at the itineraries you are basing yours on

Day 2
10am Ghibli Museum, Mitaka - until 1:30pm
1.5 hours journey
3pm Asakusa - until 5:15pm
15 min walk
5:30pm Sky Tree - until 7:30pm
Oshiage station to Shimbashi station - 20 mins
8pm Shimbashi area

Day 3
10am Ueno area - depart from Ueno station at 12:50
the blogger mentions Nezu temple but it’s a 30 minute walk between Nezu Temple and Ueno station
this actually means that out of the allotted 2 hours and 50 minutes for this area, more than half of that time would be spent walking to and from the attractions
ITINERARY WARNING - NOT REALISTIC
10min journey time Ueno to Akihabara
1pm Akihabara - depart 3:45pm
Is two and a half hours enough time? Hard to say, if you hate Akihabara it is too long, (or maybe not if you have lunch there), if you love it, not nearly long enough.
4pm Yurakucho and Ginza. Not mentioned is the Tokyo International Forum nor Tokyo Station. The newly opened Yaechika underneath the West side of Tokyo Station is also proving to be a very popular tourist destination. Hardly matters as the suggestion is to spend a paltry 1 hour and 40 minutes in the area. - depart 5:40pm. Again:
ITINERARY WARNING - NOT REALISTIC
20 mins journey time Ginza to Roppongi
6pm Roppongi Hills

Day 4 is fine once you get to Shimokitazawa. My own experience of Tsukiji Market is from years ago before it moved to Toyosu Market.

Day 5 - Odaiba and Tokyo Tower. No and no.