Not familiar with warrior epic but barring exceptions you don't need to work on faction for epic outside quest steps. In the shaman case it is so you don't just show up to rak'ashiir with your iksar tear and be done with it. Enchanter epic doesn't have faction AFAIK but like almost every single step is combined into a bag for the turn ins so you can't really MQ/skip anything.
If you haven't killed major quest NPCs and follow the progression I think you'll be fine. Best way to double check is to hail the mob and go through the dialogue. If he gives you the quest you're most likely fine. Like for the sash/headband part of the monk epic if you don't have the silent fist(?) faction they'll tell you to come back when you've proven yourself if you go through dialogue.
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