| Carpal Tunnel is caused by using sharp angles in your wrist when you're working your fingers. All those pads and stuff you see for keyboards and mice are designed to keep your wrists straight as your typing. Carpal Tunnel Syndrome is VERY common in people who type a lot.
Think of it like you're weight lifting. Your arms burn, but you keep going. If you use improper form you can seriously hurt yourself, but it's perfectly normal for the muscles/tendons in your hand to ache and your forearm to burn during intense practice. If you feel your WRIST start to hurt, you need to rethink your form.
When I do my morning routine, usually by the end of the session I can hardly play. | 
