I must confess that I have some discomfort diagnosing your problem via e-mail, without even seeing you. I feel kind of like a radio talk show doctor. But I'll give it my best shot.
A couple of the things you describe seem incorrect. There should be no strain on your thumb whatsoever. It sounds like you must be squeezing your thumb on the neck. Your thumb should only be touching the neck lightly. Your thumb should be naturally curved and lightly touch the neck opposite the middle finger (approx).
If your index finger is in pain, you must be trying to force it to go into an unnatural position. Are you trying to create extended position by spreading your finger to the side? Perhaps your fingers are approaching the fingerboard at too much of a right angle. You may find it easier if you tilt your hand a little back. In other words, the thumb side of your hand is a little lower than the pinky side. In this position, when you lift your first finger, you are almost doing extended position automatically. Your fingers move more naturally with the lifting motion than they do with the spreading motion.
Remember that extended position is putting a whole-step between your first and second fingers. The other fingers remain in the same relative position. In non-extended position, there is only a half-step between your first and second fingers.
When extending forward, make sure your thumb is loose. When you move the 2nd, 3rd, and 4th fingers down, your thumb should slide with them. And remember to have your hand tilted back a little so that your first finger can be moved away from your other fingers in a more natural motion.
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