Chiros I know say that any leg length discrepancy over 5mm should be treated with a lift.
Whatever you do, do it all the time. Don't wear a lift for school/work, then lift in your Vibrams (I'd say don't squat in your Vibrams either).
My advice would be to keep doing the S/I adjustments yourself, do DeFranco's Agile 8 at least every leg day, find a massage therapist who does fascial work (NeuroMuscular Therapy, Rolfing, whatever), and be consistent in either wearing a lift or not. Also, I don't have any particular evidence for this one, but I'd highly suggest avoiding gluten/dairy/nightshades and any other foods you are sensitive to.
I used to have about a 5mm leg length discrepancy. It has seemed to have gone away (or at least my symptoms I associated with it) about 90% by cleaning up my diet. FWIW.