OK I have a reply for you OP
I would be grateful for answers to any or all of the questions below!
I've found some great value tickets with Air China. Is it ok as an airline? I can cope with it not being the most luxurious travel experience, so long as it's basically safe and reliable.
I can't comment, but Im travelling with them soon so fingers crossed!
I don't want to be over-ambitious, so am planning to spend roughly a week in Tokyo and about a week in Kyoto/Osaka with possibly some day trips. I'll probably be doing the trip solo and it's quite tiring working everything out on your own, hence mainly doing those two cities. I realise I'll only be getting a flavour of the country, but would I be missing anywhere absolutely essential that I couldn't accomplish as a day trip if I plan it like that?
I wouldnt say so. Osaka and Kyoto are pretty close (about an hour by train if memory serves), pretty earsy to spent time in both. One thing I feel i should memtion is that recently, due to torists behaving badly, certain parts of Kyoto's historical geisha district, Gion, have introduced ban on tourists entering. Please be careful and hyper aware of any signage.
Should I be looking for any specific type of accommodation? I.e. in Morocco I would recommend a Riad rather than a hotel. A ryokan? Capsule hotel?
Ive always stayed in Hostels (kinda like capsule hotels but less fancy). You can save a lot of money staying in a hostel, but there are downsides (lack of space, shared bathrooms). First, I'd decide if you'd be ok with a hostel or not. Then look on book.com (other comparison sites are available) and find do a search based on hostel/hotel and a price range. Find somewhere youlike the look of thats close to a train station. Japanese cities have great public transport. Being near the city centre is good, but not essential, but also make sure you're not way out in the suburbs. I cant say much for Osaka/Kyoto, but in Tokyo you might want to look at the areas of Asakusa and Ueno for accomodation. I've satayed at a place called Hostel LodgingTokyo Minowa (Minowa is the name of the area) that was nice. As for ryokan, I'd say youre paying a little more for the experience. If you want to try it out, maybe been one night but spend the rest of the time in a hotel/hostel
Anything amazing that isn't on all the lists of obvious must-sees?
Nothing springs to mind. Decide what you're into and go do that (sounds obvious, I know)
Will I manage with very basic Japanese? Is it worth trying to learn hiragana? Basic phrases? I did a short course and am planning to continue with Duolingo until I go (probably in October).
Japan, in my experience, is pretty English friendly. Signs and train info is usually in both. I dont think learning Hiragana will help much for this trip (its mostly just used for grammatical functions), but if you're planning to learn the language its essential. Yes to basic phrases, very helpful. Id recommend downloading a translation app like google translate or Wooask. You can trype in something in English, get a translation and just show it to the person (or try to say it if you're feeling confident). These apps also allow you to take photos of written japanese and will give you a reasonable translation. Lots of places to eat will have english language menus, buts the translation can be a bit ropey sometimes. Also be aware that here's a move in japan right now towards 2 tier pricing for visitor so things on the english menu might be more expensive than on the japanese one.
I'm a bit confused about onsens - do you also stay overnight?
Some Ryokan will have onsen baths onsite, but most onsen and just for visiting, not staying. Theres also things called sento with are public bathhouses too. The difference is that sento just use 'normal' and are are more for getting clean, while onsen use geothermal water pumped from underground that have minerals in and are usually for relaxing and some possible health benefits. If you're planning to go to either PLEASE read about the rules for using an onsen or sento. A quick google search will bring up plenty of infor, but please take the time to learn about it.
Any other tips, like anything particular I ought to take?
Not really, pretty much anything you need you can get in Japan.
If I do the journey I'm planning I will have a 20-hour stopover in Beijing so I'm hoping to go into the city for a few hours and then stay overnight in a hotel. It seems I can do this without need a visa. Can anyone confirm this, or confirm I've got it wrong? (Please only answer this one if you're absolutely positive one way or the other!)
Sorry, I'm not sure about the visa but I was reading the other day that if you have a long layover in Beijing, China Air with put you up in a hotel for free. Worth a quick search.
Extra -
Always carry your passport with you everywhere. Japanse police can and will ask to see it (happened to me in osaka once). You can be arrested if youre not able to show it.
This may seem obvious, but don't follow touts. If a man (and its usually a man) approaches you to get you to come to their bar or club, DON'T. Ignore them and walk away. There are many stories of tourists being drugged and having huge charges put on their credit cards.