Always book a hotel (or AirBNB) close to a Yamanote line station. 90% of attractions are along the Yamanote line.
Nakano broadway is worth seeing if you like older anime from the 80s and 90s.
For cheap used retro games, anime goods etc go to Bookoff. The well known stores in Akihabara like Super Potato etc are a bit of a ripoff.
If you want to visit the Ghibli museum, you need to book it at 10AM (Japan time) on the 10th of december. Tickets sell out in less than an hour. Found the museum to be slightly underwhelming though, personally.
Nah you can only book a month ahead of time. OP, if you're in the US, that's going to be anywhere between 19:00 and 22:00 on the 9th for the booking, depending on what part of the US you're in.