1. TMB observatory opens at 9:30am - not that near Shinjuku station (nearer Tochomae station). Brave the rush hour and aim to be at Shinjuku station around 9am to get there for opening time. Depending on queues to lift it will take between 5 & 20 minutes to go up and then again to go down.
Assuming you get to Tochomae station for 10:30 it will take around 10 minutes to get to the platform, 15 mins journey then another 10 minutes to re-emerge at Akabanebashi and 15 minutes to then get to Tokyo Tower.
2. 11:20am Tokyo Tower (why?) and Zojoji temple (never heard of Zozoi temple).
Let's assume that seeing both takes an hour
You'll need at least 30 minutes to get from either to Tokyo Station by foot or train unless you get a taxi.
3. 12:50 Tokyo Station. From here to Imperial Gardens takes around 15 minutes.
Then you plan to back track to Harajuku (which is best seen on a Sunday)
Between 10 & 20 mins to get to platform, 20 minutes to Harajuku = approx 40 minutes.
3. 14:30 arrive Harajuku. Getting between Harajuku & Shibuya will take between 10-20 minutes depending on whether you walk or take a train.
Shibuya to Asakusa takes 30 minutes plus getting to to/from platforms, waiting for train. Assuming you spend 35/40 minutes in Harajuku and 35/40 minutes in Shibuya.
4. 16:40 arrive Asakusa. Leaving at 17:40 to arrive at
5. 18:20 at Shibaurafuto station.
Count on 15 minutes journey time plus at least 20 minutes getting to and from platforms to get from Shibarafuto to Tokyo Shinkansen platform. You may just be able to get back for a 19:30 departure to Osaka.

Not an itinerary I'd recommend at all. No time for something to eat, no time to use the toilet, no time to enjoy what you do see. Unnecessary zigzagging across the city. Huge potential for disappointment with chosen attractions.

Hopefully you can see for yourself what kind of day you are proposing to punish yourself with.
I'm with NickW - compared to what you've planned, the bus tours look very enticing.