This is genuinely good. I've always avoided upscaled backgrounds in the past, because I felt like the scaling artifacts, the weird blotches, etc., looked worse than the pixellation of the originals. This is the first attempt I've seen that I would actually use myself.
It's not perfect; among other things, some of the higher contrast dithering still scales weirdly (most obvious with the back wall near the top in the first screen). Have you considered running a low-strength noise removal filter over it before scaling? I've found that Photoshop's noise removal is pretty good at blending dithering like that without eating away at detail. For example, using
these settings, I processed that same screen and came up with this:
At this size, the original size, the difference is virtually indistinguishable to the naked eye. But with the dithering blurred, I'd imagine this would scale much more nicely with that improved scaling system you've got set up. Just a thought, maybe worth trying. If you don't wanna put in the effort of preprocessing fields through Photoshop, I certainly won't blame you, and I can't guarantee that the results would even be as good as I suspect they would (I don't have waifu2x handy to test it myself right now). Still, it could be worth trying.
In any case, what you've got is already so much better than anything I've seen. I'm really excited to see where this goes. I'd use it.