For the code 90, make sure your gas cap is on tight. Then reset your ECU, and see if the codes come on again.
As far as the rough running, check your firing order on the distributor again and make sure it is correct. If it is not, the car will run and idle terribly.
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2015 Ford Mustang GT Fastback - Ingot Silver - 6M - Performance Package - Gibson Catback, JLT CAI, FR 47lb injectors, BAMA E85 tune, Eibach Sportline, BMR wheel hop kit, UPR oil separator, Steeda shifter bushing/bracket
Team B.O.B.® - Ballaz on a Budget