I would definitely hold fire on flights for the moment. Virgin are quoting £720, which is about £200 more than you should be paying! Alternatively, there are courier flights (usually with BA) which involve transporting a document to give to somebody at the other end, and those can go as low as £250. I've never done it myself, but I know plenty who have and have recommended it. In fact, sometimes there isnt even a document to take, so it just becomes a very cheap flight!
Well priced hotels is a bit more of a challenge. While it seems sensible to get a hotel as close to the start or finish as possible, most places in Tokyo are easily accessible by the reliable (and frequent) Metro system, so as long as you're near a station, most places are pretty easy to get to. Shinjuku, Iidabashi, Ginza, Shinbashi, Shinagawa, Akasaka... they're all good places to stay.
The course is pretty good. The first 6 miles is all downhill so if you can get into a decent rhythm there, it sets you up nicely for the next 14 which is fairly flat (a few little bumps here and there). The last 6 is quite challenging though so its worth keeping something in the tank. The first bridge off the mainland towards Odaiba is especially severe. The uphill section is only about 150 metres long but its quite steep and can sap your legs a bit. After that, you have to go over a few more bridges (so a few more ups and downs) then twist and turn your way around Odaiba before hitting the finish. The support around the course is also fantastic and the volunteers are always happy and helpful.
My only gripe was toilet facilities. I hope they get a few more in place this year. I know somebody who queued for about 5 mins to use one! But thats just nit-picking though.