After collecting witch heads I returned to the Companions base in Whiterun to find that the Silverhand had attacked. I've tried talking to all the members to receive my next quest, but no one is responding to me whatsoever. There are no new dialogue options for the few members that will even talk to me (all of them outside the building). This happened a few days ago: Today when I returned I noticed an additional glitch where there are two Farkes', one standing by the dead old man and the other sitting near his body.

Also, every now and then when I enter my Whiterun house, someone else appears inside as if they walked in with me. So far a random citizen and one of the guards have showed up. They turn around and walk right out as soon as I'm inside however.

I'd reload an old save from before you returned to Whiterun. That sounds like a bad glitch.