I've never been to Seattle, but I agree SF is expensive. (I have family there, so it's another place I got every few years, though we see my family in SoCal more often.)
Kyoto and some of the smaller cities with enormous festivals can book completely up, but usually not for a 60 mile radius. But presumably you've already booked your accommodations for Kyoto. I find cheaper places go first, there are a lot of budgetary travelers in Japan. If you want somewhere with a good location and I think $130 or so a night, I would recommend the Royal Park. It's rated very highly for the most part. I came really close to staying there again.
Maybe for the Olympics Tokyo will have a shortage of rooms, but for normal touring times that isn't a problem. I've booked hotels a couple of days out when I was less picky. I've not been to Rome, but Tokyo is much much safer than Paris and London. The biggest dangers in Japan involve just being aware for natural disasters but if you live on the West Coast, I'm sure you've thought about those already. I have been in Tokyo/Japan for quakes. They can be a bit frightening. Japan is not some sort of paradise but in Tokyo the most usual crimes you might encounter are: men peeing in public, men puking on trains, and there are men who will grope women on crowded trains. You also might have a train/subway delayed due to a suicide. Yeah, people still jump in front of trains there. If you see a delay because of a "human accident" it means a suicide. Actual violent crimes are just so rare. While visiting a friend in Nagoya, one of the big news stories which was repeated several times, was an angry salariman had used his umbrella to decapitate a huge amount of tulips in a public space. This was a big deal and the police were looking for information on this man. It's just a very different culture with different expectations. Concerns about a smoky room or smoky lobby are real concerns. Concerns about ventilation or lack thereof, I can see as well. But concerns about robbery or other violent crimes... not so much. The only regular "theft" is umbrellas.
But you should still use some common sense. Random cute girls who want you to take them back to your hotel or buy them drinks or are a little too friendly are usually something to be wary of. It's not a problem I've had being female and not the hanging out at bars or night clubs sort of person.
Me, first trip to Japan I knew maybe 3 words of Japanese and I was going on my own. I'd gotten married rather young and had only been to Montreal for a long week end by myself. I stayed in Tokyo. Went up to Morioka and Kakunodate because... I could? Went to Licca Castle, went to Kyoto and went to Wakayama Castle. I met a few friends of friends while there, (who I'd never met in person before) but really did most of it on my own. Eating alone can be lonely, but that was about the worst of it, well and the cold I picked up... You're actually quite lucky, now there are smart phones and gps so you're not likely to get lost. Japan might seem daunting, but it's actually one of the better places to be a solo travel.
I'd offer to meet up but we're missing you by about a week. I am sure you will have an amazing time! ^_^