1. Water is flowing in the correct direction.
2. Will fix that.
3. Geiger counter sound is a commonly used trope in video games to signal radiation. It's used though the entirety of Half Life 1 (and Black Mesa), the Fallout series and all over bomb crates at A Site Nuke and A Site Train. It's also present in Sub-Zero near the green goo pipes.
4. Will look into that.
5. It's a game. Random wood panels and scraps add detail and character. Sorry if you didn't like them, but they stay.
6. It's possible the terrorists lit the torches on their way up. And maybe things are being brought from the cave to the elevator, not the other way round. Anyway, no solid answers here as it's up to you as the player to imagine what might be going on. It's not really relevant to anything, but the theme of the map is science fantasy fiction, so a mild suspension of disbelief is not too much to ask.
7. As I said, it's science fantasy fiction, a location isn't necessary. It can be wherever you want it to be. Is it going to change anything if I set it in the Himalayas, or an island in the Azores? I don't think so. The named scientists are so named because that is T-Rex's and my IRL names. Sort of a 'credits' if you will.
I think most of these 'issues' are minor nitpickings, and wouldn't actually add anything to the map if they were 'fixed'.