Could be a number of things (neck position, hand position, thumb position, etc.). Instead of getting the pinkie out of the way for runs use the pinkie during some of the runs. Perhaps just practice fretting sequence 1-2-3-4-3-2-1-2-3-4-3-2-1-... until reasonably fluid.
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Derek Coombs
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Guitars by Mark Blanchard, Albert&Mueller, Paul Woolson, Collings, Composite Acoustics, and Derek Coombs
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