1) I think Obsidian just forgot about Hanharr and there was nothing to restore.
2) Same problem with Bao-Dur, I believe that at one point Chris forgot about Bao-Dur and just stopped his arc there.
3) The way to unlock the HK-50 factory is to ask HK-47 if he knows anything about the Sith hunting you and then he brings up the Sonic Emitter from Peragus. Once he figures it out he can use it to track the HK-50s, you have to bring HK-47 with you wherever there are HK-50 ambush squads. You need to bring him to at least three encounters until the criteria is met for unlocking the HK-50 factory. (Don't worry - you can't do it as soon as you find out where it is. Just keep playing the game and the HK-47 solo mission will naturally occur. Be sure to craft/buy the best equipment for him, as the Factory is no pushover). Trust the alternate HK line, once you will reach that part.
4) I... don't have a lot about that in mind, generally speaking the Light Side story line makes more sense.