Do you ever have the pain when you use your little finger elsewhere on the fret board? I can't remember its placement but Justin had a stretching exercise (think he called it "spider walking") where you start on the low E, first finger is at fret two, middle on three, ring on four, pink on five and you walk down the guitar playing all four notes on each string. Not sure if you've gotten there yet or tried this exercise, but my guess is that you'll find some pain on that one too if it's not technique related.
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