After installing the GOG version I noticed that it's noticeably different from what I remember and not in a good way (squashed menu font, bugs, dialogue typos). I then noticed that it comes pre-installed with a high-resolution patch and a TEAMX patch. Is it possible to remove them for a clean install? If so, how?

If it is squashed, just tweak the settings. That's what they're there for.

Two problems with that:

1. I already tried the mod launcher and the config files, to no avail.

2. I'd vastly prefer to play an unmodded version. I think I'll just dig out my old CD and reinstall from that. I think it's a real shame that the GOG version includes mods by default and doesn't even give the option of not installing them while installing the game.