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The problem you've got is overlapping transparencies. The engine is not able to get your GPU to render them correctly. This is likely a legacy problem stretching back to the game's launch, where it was known to have problems with then ATI GPUs. It also stretches to various other rendering issues across all GPUs for various things, but those are less noticeable for most people. Aside from installing the DX redistributable if you haven't already, I'm not sure there's much more you can do on your end. The only practical permanent/universal solution would be for @Kexikus to replace that background alpha'd plane with actual cutouts of the buildings so that there is no alpha masking is required.

I didn't upscale those. There was a higher resolution texture for the Revan robes elsewhere in the game files. For Bastila's clothing, only the missing shader data was added, and the texture wasn't changed at all. I would recommend waifu2x for upscaling, though. I've used that in other mods before. The grain remover makes it lose some of the detail, so I often add my own texture overlay to get it back. There might be better GAN-powered solutions that have come out more recently, but I've yet to look into them.