Whistle Stop, Thanks very much for bringing up the carpal tunnel issue. No one should inflict serious injury on themselves to play music. As you rightly guessed, the pain I was referring to is that caused by stretching in a new way to make an unfamiliar chord, or maybe the pain in one's finger tips; the sort of pain that can be "worked out" through exercise.
Guitar Exercise Tip:
A good way to warm up your hand and improve it's ability to make long stretches is to play scales. A two-octave scale in A beginning with the middle finger on the fifth fret of the bass E string is a good warm up exercise. Each noting finger covers only it's "assigned" fret with the middle finger assigned to the fifth fret. Work the scale up and down without pausing. If you have never done this, you will soon feel your hand tiring. Some players carry a small firm, but not hard, rubber ball with them and use it for finger exercise throughout each day. Books have been written outlining specific exercises with the ball although none comes to mind at the moment.
No pain, no gain.