Question 1: My NPC has Confidence set as 2 (Average). How can I increase this? Modav doesn't seem to work, at least through console commands.
Question 2: I want to add Energy Weapons as my NPCs tag skill through dialogue. What command should I use?

EDIT: On question 1, confidence is intended to be just Average at first, so editing the NPC directly is not an option.

Edit: I got no results. I thought I would.

Answer 1: SetActorValue works. I just tested it, both in console and in script. The range for Confidence is only 0-4, so setting it explicitly shouldn't be a big deal. Incidentally, the fact that the range is circumscribed may be the reason why modav doesn't work on it. (I tested as well in console and script and it didn't do a thing for Confidence.)
Answer 2: At a quick glance, there doesn't appear to be an option to set a tag skill on an NPC, but you should be able to use modav on the skills. Just deduct points from one and add them to the other.

I'm not a scripter, so someone else may have better answers.