I had Farkas following me when we did the quest "Hard Answers" at Markarth. I had a really high bounty as I went into the museum when I wasn't supposed to; I killed a couple of guards, turned into wolf form, got what I needed and ran until I was safe. I assume Farkas was probably fighting guards inside the museum.
I waited a couple of days before going back to Markarth (so I would not be attacked anymore) and Farkas is no where around. I do not want to look for him in the museum because that will start a huge mess again. I have also looked back at Whiterun (his home) and he is not there. I have tried to ask other people to follow me like Vilkas, etc, and they say "looks like you already have someone with you".
I have tried all of the techniques: Wait a week, fast travel, go to their home. I can't load the game before it happened though because I do not want to do all of this quest stuff again. Any suggestions?