After what seemed like an eternity of aches and pains when I rode (butt pain, back pain, hip pain, neck pain, hand and wrist pain), I finally broke down and saw a licensed physical therapist who does bike fittings. She discovered, among other things, that: 1.) my right knee tracked perfectly over the pedals, but my left knee splayed out a full 17 degrees; 2.) my brake hoods were angled slightly outward instead of inward; 3.) my saddle was 2 cm too low; and 4.) the SPD cleats on my shoes were positioned too far back.
She also did a functional assessment of my range of motion, strength, etc. She found that my left hip/glute is considerably weaker than my right, and she prescribed exercises to compensate for that.
I've ridden much more comfortably since then. The bike fitting was $200, the assessment an additional $100. I consider it to have been $300 well spent.