I believe that this falls on the right side of incidental vs. expert knowledge and that, while it's not exactly within the topic as defined by the site so far, it is something we can and should be knowledgeable about.
In many games, at sufficiently high levels of play (= expert!), being part of a functional guild in an essential part of playing videogames. No strategies, tactics and game mechanics knowledge can help you if you're having communication and organizational issues and your carry is too busy calling people names on all chat while micspamming on Mumble to actually play.
One of the long time tenets of Stack Exchange is that opinion without experience is noise. So long as we can find answerers with experience, we should be able to give good subjective questions an expert answer.
That said, some of your questions are really kinda broad. You'd have to specify a few things first:
- The style of your clan (primus inter pares or strict hierarchical? hands-off or strict enforcement? how are you willing to sacrifice clan morale to boost results?)
- The clan management tools you have at your disposal (what tools and knobs do you have to reward and punish behaviour?)
- The game itself (at least in terms matters of community size, growth and style, plus the kind of events your group does: PvP, PvE, both, something else?)
Take your question about misbehaving members: if your guild is a TF2 Steam group, all you can really do is demote from officer (if officer) or outright kick people off your group. If you're playing competitively, you might be able to force them to bench a few weeks, perhaps? but if the misbehaving person is actually the Steam Group founder, you might be SOL short of going thermonuclear and leaving/forking the clan yourself. If, instead, you are a high-level WoW clan, you have more powerful tools available to you, such as loot distribution parameters and other things I'm not aware of since I don't have WoW experience and my opinion is noise.
The main challenge here is going to be striking the right balance of scope:
- How can I deal with misbehaving people? (too broad)
- How can I deal with my niece calling my girlfriend's wardrobe-shaped brother names on my brother's Minecraft server? (too specific; also, the asker is powerless in this scenario)
- How can I deal with people being constantly negative to each other? (probably okay, with the caveats above)
We can't, shouldn't and won't write the book on guild management. We can't, shouldn't and won't review specific cases of abuse, no matter how nuanced and complicated they are. However, if you give us a reasonably specific yet generally-useful scenario, we could, should and... um... should want to help you.