Just so that you're aware, using certain scaling/filtering methods alone might not be considered "custom" enough for a custom/HD texture project. If you're wondering what I'm talking about, have a look at
this discussion on a recent matter. However, before I go on, I don't think your project has anything to worry about (explained more below) so before you start sweating, this has my seal of approval, no worries.
Anyway, what it boils down to is that we shouldn't have custom/HD textures that too closely resemble the source textures so that we can avoid infringing on copyrights (and NIntendo loves a good DMCA takedown). E.g. scaling filters do enhance an image, but they often follow the source material too closely, for example, keeping noise or compression artifacts, or edges that should otherwise be smoothed when upscaled. Situations like that makes the "new" texture only slightly distinguishable from the source, which in turn goes back to copyrights and that sort of trouble. So in essence, we're looking for custom/HD textures that are "transformative" enough.
But, as noted in the discussion I linked to, it's on a case-by-case basis that we look into these things. The ones you drew in GIMP are fine, no problems there (they look amazing btw especially that wanted poster). The blob textures made by waifu2x look fine to me as well (a lot of noise has been removed, and imo, looks like an artist redrew it rather than a neural network). The granite textures slightly concern me, if only that the differences aren't very apparent until you view the 512x512 vs 2048x2048 version. Again, it's impressive what waifu2x can do; it literally added texture/depth where there wasn't any in the source. So in short, I think waifu2x manages to be "transformative" for this texture pack since it adds artistic elements not present in the source. Other scaling methods (such as xBR) don't particularly do that, which is what we're concerned about, from a legal standpoint.
Shonumi ~ 2016 - comment link:
https://forums.dolphin-emu.org/Thread-super-mario-sunshine-uhd-texture-pack