I feel most of your questions seems to be answered
hope you'll have alot of fun.
I think whether you stay in Ueno,Shibuya etc. will not matter all that much, both are very nice places to be. And on the Yamanote line which is really good. Otherwise travelling by train or subway is not hard in Tokyo, just get a train/subway map and you should be able to figure it out, and when you can't, people will help you if you ask.
If you are here on a sunday, I recommend you to go to Harajuku and enjoy the day there. In the area just at the JR Harajuku station (yamanote line) and around the entrance to Yoyogi park (close by) there is just so much fun and life on sundays!