1. These "upgrades" are called skills in game and they go in the top right section of the girl's info page that you can get to from the menu. The ability to edit their skills unlocks at 3 hearts.
2. The AI is intended to be this way, you are either supposed to let the AI learn on its own or teach each girl individually by doing things like sleeping and gathering while they are following you. The second method, having them follow while you gather things or sleep, is much faster.
3. Unfortunately, I don't have an answer to this one as the only mods I use are in the repack. I don't go out of my way to get any because I don't want to take the possible risk of adding a mod that conflicts with the ones I use from the repack with a completely unknown probability of finding one. I was going to recommend sites at least, but you said you went to the ones I was going to recommend already.
If your posts are deleted, you should be getting a notification in the top right and it should explain why. I've had a few WTF deletions over the last month myself and nearly every single one was for going off topic when I specifically kept them in relation to the game of that thread.
