Try to be consistent with where you get fuel. I have had a view bad tanks from sheetz and will never get fuel there again. I had shutters and misfires and now that I only run Sunoco with lucas fuel injector cleaner every 3 or 4 tanks, it runs like a gem. If it happens again, maybe try some seafoam as you could have some gunk built up in the intake and valves. Glad it is back running well. Got to love the 5 speeds.
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MINE - 97' SR5 manual (Desert Dune Metallic)
HER's - 14' limited (Altitude Black)