It's ScaryWell, yes, and being the anxious type doesn't help. But Tokyo is such a breeze. You don't need anything but the yen in your pocket and the English in your head, and you're solid. There's so many signs and info kiosks and hand-holders in Japan that it would be pretty difficult to get into trouble
English is so often added to everything in Tokyo, so you can't get that lost. If you're heading towards the countryside, into the mountains, or off to find the source of your favorite Earth Porn picture [Yakushima Forest], maybe be a little more careful about writing down Google's advice on how to get there. Write out the kanji. Or stick to Tokyo and Kyoto and Osaka and be free of any fear.
The Woman AloneNope, you'll be fine. Crime in Japan is ridiculously rare. People leave their purse behind when they go to the bathroom to show that they'll be back. In Tokyo. At night. I walked around Akihabara at night to go play arcade games, and I didn't sense anything scary or suspicious. If you're around late enough in Tokyo, the main hazard is avoiding drunk barf.
But I've heard people talk about the cheap deals on love hotels as an accommodation type. But I'll be over there, in safe town, in my boring little Airbnb with no red hot tub, and that's okay.