OK first off, I think you are kind of limiting yourself when you just want to spend time in Akihabara.....it's like saying "we just want to spend 2 weeks in Covent Garden" it's just a small area of Tokyo, which in itself is just a small area of Japan. You have 2 weeks, explore as much of Japan as you can, Kyoto and Osaka are just 2hrs away via the bullet train for example. Japan has a lot of things to offer and if you really want to experience Japan you need to see not just the "otaku" side of things.....Kyoto would be my ideal recommendation along side the high tech part of Japan.
On to more pragmatical things, capsule hotels cost roughly around 3,000 to 4,000 yen a night (£15 to £20...ish) Ryokans (traditional Japanese Inns, kind of like a British B&B in a way) cost a little more....
I'd recommend 2 websites
www.gendai.co.uk
this site is where I've found the cheapest airfares, and I think they can organize cheap accommodation for you too.
http://travel.rakuten.co.jp/en/
this site is useful for booking hotels cheaply....I use it all the time to book hotels for my business trips over here, for the most part the hotels that I book average around 6,000 yen a night and they are fairly comfortable...more so than a capsule hotel
At the end of the day......don't come over here with too many pre-conceptions...you will be disappointed....have fun, and make sure you try as many different foods as you can at least once.