Submitted for your approval my itinerary. I'll be flying in on a Monday at 2PM and leaving the following Monday in the morning. My budget will probably be $1,000 USD with hotel and JR pass already payed for. I'm putting a $200 limit on my shopping because I don't need to bring a bunch of junk back with me. I'll be traveling alone.
Monday: Arrive and head to apartment near Nishishinjuku Gochome Station. Head over to Capcom Bar and put in a reservation time. Go check out Book-off, traders, and Sofmap. Eat at Capcom bar then catch the last show at Robot Resturant.
Tuesday: Head over to the Eorzea Cafe at around 10 am and reserve a slot. Explore Akihabara (Animate, White Canvas, Book-off, Super Potato, Melon Book, Toranoana). Eat at Cafe then either go back to apartment and drop goods off or just stay in Akiba and play in the arcades (Hirose Entertainment Yard , Club Sega)/catch a movie, ect.
Wednesday: Head down to Odaiba and check out the Gundam Museum & Namco themepark. Scope out Joyopolis and the surrounding area and then possibly go back to Akihabara if I want/check out Nanako Broadway. Visit Shibuya crossing and have dinner at Ninja resturant.
Thursday: Head to Universal Theme Park in Osaka. Check out Den-Den town, Osamu Tezuka museum & Osaka Castle if time permits. Head up to Kyoto and have a couple of drinks at Cafe La Siesta then call it a night.
Friday: Check out Fushimiinari and Kinkakuji temples then head back to Tokyo and maybe catch a movie if anything interesting is playing.
Saturday: Nanako Broadway and any other shopping that I want to get done. Check out Ginza & Roppongi
Sunday: Go to Harajuku & Yoyogi Park and people watch. Make one last trip to the arcades.