Itinerary squence

I need advice on the sequence of my itinerary

Travel dates 16-23 Apr. Staying at Ikebukkuro.

Sat 16/4: Shibuya
Sun 17/4: Harajuku
Mon 18/4: Disneyland
Tue 19/4: Disneysea
Wed 20/4: Asakusa/Sightseeing at some parks in Tokyo
Thur 21/4: Visit cat cafe & shopping
Fri 22/4: Hot spring is there is in Tokyo
Sat 23/4: Any advice?

I need advice for my trip sequence. Want it to be cost effective meaning so i won't spend so much on transport fees on the subway.

i would like to make some editing.

Sat 16/4: Shibuya
Sun 17/4: Harajuku
Mon 18/4: Disneyland
Tue 19/4: Disneysea
Wed 20/4: Asakusa/Sightseeing at some parks in Tokyo
Thur 21/4: Visit cat cafe & shopping
Fri 22/4: Meiji shrine/Hot spring is there is in Tokyo
Sat 23/4: Shinjuku

any advice on nice and must-go places that i missed out?

The hot springs in Tokyo don't provide the "authentic" hot spring experience, being sterile, artificial and overpriced (although cheaper than making a journey to a real hot spring resort).

If possible, I recommend to make an overnight side trip to a real hot spring resort nearby Tokyo and stay at an onsen ryokan. Some of the better resorts are listed here:
http://www.japan-guide.com/e/e2292_resort.html

you could do Shibuya & Harajuku on the same day and have a day to do something else. (Harajuku is more fun on sunday) Everthing else is do-able. If you want a real onsen, you will have to travel ouside Tokyo. If you want a theme park like onsen you can try Ooedo Onsen. http://www.ooedoonsen.jp/higaeri/english/index.html

probably didnt spell that right,

you cant go tokyo and not go to the akibhara district.

yes there will be otaku, but thats part of the fun.

for meiji shrine, on which day do people get married there?

Especially Saturdays and Sundays that fall on a Taian. Probably considerably fewer on Butsumetsu:
http://en.wikipedia.org/wiki/Japanese_calendar#Rokuy.C5.8D

judging from the places i go in my above itinerary, what is the estimated amount that i will spend on food and subway for 2 pax?

food will be those budget kind.