Normal PCSX2 render for comparison.
So far so good as proof-of-concept, but still looks like just applying a shader to the whole thing instead of upscaling individual items. So my plan is to later clean up all of the pieces by hand so that it looks like a proper HD version.
WIP Shot 01: Cleaned up some of the alpha channels, and detailed her eyes. And yeah, got to see some bugs when it's in motion.
That's all for now. I later found out that TexMod has been succeeded by an open source project. I will look into it and see if I should upgrade to that instead of the original TexMod.