I have asterisked out quests where you just need to find information. They are not strictly necessary, but they are neat puzzles. They may require knowledge found elsewhere in the game. If you really need to improve affinity just talk to someone, cut off the conversation, and talk again. That's one affinity point.
Agility comes from fixing or using weapons, and intelligence comes from fixing or using items.
They're not worth it. Boost labs are too hard to get to although they are a neat puzzle. Look for Fritz in the underground. The first thing to do is to go to Joe's Bar. It's a building north and two to the east of where you start the game.