Well its great to have a plan but if you don't make it to half of what you have down each day then you will have accomplished and seen quite a bit. I've been to Tokyo many times and would find it hard just to get to the places you mentioned each day. You need more time to savor and explore these areas you mention and not just get there then move on to the next venue.

Aloha!

Let me give you and example of what I mean and how day 1 may go for you

You are starting out of a Shinjuku hotel I am presuming. Isetan will open probably around 9:00 am or later on a Sunday. You will be there for at least a half an hour or more checking out the food. You buy your food and if you can resist the temptation to shop more in the other ten stories of this mega shopping store then you walk over to Shinjuku-Gyoen Park I am presuming again. That's at least another 30 minutes as you pay to get into the park and maybe eat your food. This park is HUGE and well worth your time as you will see. It's one of my favorite places in Tokyo to "get away". I usually do a walk around the park which takes us at least 2 hours. Then it would off to Yoyogi Park. Depending on which exit you take from the park, it will take you at the least 30 minutes to reach by foot then either subway or the JR Yamanote line to Harajuku station. I would guess that it would take you more than an hour to get there as you will still be on the learning curve and getting lost or turned around. Then Yoyogi Park will involve at least three hours as the place is HUGE again with lots to see and the flea market only enhances your time there. I would be exhausted about now and heading back to my room to freshen up for dinner and a night out on the town but that is a look at how time can fly in Tokyo. Hope I made some sense.

Aloha!