While it may not officially be "Carpal Tunnel" you probably have some sort of repetitive stress injury (RSI) (PS I'm not a doctor). I had a mild brush with it back when I started computing. After an hour or two at work I couldn't use one of my hands.
I had several months of physio and luckily recovered. But it can flare up if I'm not careful.
By careful, I mean working at an "ergonomically" unsound workstation.
Definition: Ergonomics is the science of designing the job, equipment, and workplace to fit the worker. Proper ergonomic design is necessary to prevent repetitive strain injuries, which can develop over time and can lead to long-term disability. (Wikipedia)
Basically it means making sure that you have a workstation and computer equipment that does not put undue strain on your body, in your case specifically your hands and wrists.
Very simply put, first you need a "proper" computing chair. Then the chair height has to be "correct" for your body. Next, the keyboard height has to be "correct" related to chair height. Finally monitor height must be right for your eye level.
My originally workstation was an ergonomic "disaster". Simply by rearranging it along ergonomic principles provided me with huge relief.
You might also want to look into things like "Wave"/split style keyboards, and alternate types of mouse pointers and wrist rests. I recently read a review of a mouse that is rotated so that your hand is in a "handshake" position rather than rotated flat. I have found that a "split" keyboard is a great help too. It took about a week to get used to, but now when I go back to "normal" straight keyboards I feel it very quickly. I've even seen split keyboards that are rotated vertically like an indian TeePee, again to keep your hands in a more natural position. I suspect they take more getting use to.
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