Is there a way to complete the independent play through whilst retaining a balanced reputation with all faction? Obviously , it is very likely there will be exceptions, but what quests and actions should I avoid(as long as it doesn't reduce rep , don't add it to the list) to get a good rep after finishing the yes man storyline?

As far as I'm aware, it's not possible to do anything related to the main story without getting a bad rep with at least one faction.