First things first:
If you are experiencing regular discomfort, take it easy. Take frequent breaks, get up and walk around, try to scale back the amount of typing and mousing you do, make sure you eat right, get enough sleep and exercise, and reduce stress and anxiety in your life if you can. If the pain is persisting or getting worse, you might consider talking to a doctor. None of us here are doctors, kinesiologists, physical therapists, etc., as far as I know.
If you think your pain is associated with mousing, you might try switching mouse hands, finding a cheap used trackball, trackpad, or roller mouse, adjusting your mousing surface, or just adjusting your workflow/software tools to require less switching between keyboard and mouse. Just getting a narrower keyboard that lets you bring the mouse closer in might have some benefit.
Try to get the rest of your workspace into comfortable shape. If your desk is too high and you can’t adjust it, the next best thing is to raise your chair higher. If you have a regular chair and a tall desk, these are a pretty nifty way to adapt,
http://www.ergodepot.com/HumanTool_Balance_Seat_p/ht-balance.htm (For me personally, a high desk and a saddle-type seat is perfect, and I sometimes take one of these balance seats to a coffeeshop where I can’t adjust the furniture if I plan to sit and type for a few hours.)
If you can’t change your chair or your desk for whatever reason, then you need to make sure that your keyboard is tilted properly to account for that. With a high desk, you want a relatively steeply tilted keyboard, so that your forearms are parallel to the keyboard surface. Flip those feet up in the back and/or prop the back end up with some books or something. (With a low desk, it’s the opposite. To make sure your forearms stay parallel with the keyboard it’s sometimes necessary to prop up the front end of the keyboard.)
Even without changing keyboards, try to type with your wrists and other joints in as neutral a position as you can manage. Especially try to avoid having your wrists bent upward (“extension”) or downward (“flexion”). Try to type with your hands “floating” with your fingertips resting lightly on the home row, without resting significant weight on your palms or elbows: this lets your whole arm absorb some of the shock associated with each keypress instead of leaving it all to the fingers. Try to keep your upper arms relatively close to your body instead of sticking your elbows way out to the side or forward, and bring the keyboard relatively close to your torso, so you don’t need to reach for it. Keep your back straight (not slouching or hunched forward) and your shoulders relaxed. Try to notice if there are particular keyboard combinations which cause strain, and change those patterns: for example, it might be more comfortable to use whole hand movement instead of wrist twisting to hit the backspace key.
Try alternating body positions, if your workspace allows. For instance, I have a height-adjustable desk and I like to switch between sitting saddle-style, sitting normal-office-chair style, standing up, and using a laptop sprawled out on a couch.
Overall, try to listen to what your body is telling you. See if you can notice which positions or actions cause you more discomfort, and figure out ways to avoid those if you can.
Now on to keyboards:
The ErgoPro or similar is definitely the easiest-learning-curve alternative to a standard keyboard – you can probably be up to full speed within a day or two – and simply splitting the board into two halves makes a surprisingly large improvement from an RSI perspective: you can “tent” the two sides you can dramatically reduce the amount of wrist pronation required to type, and this allows you more flexibility to adjust various other aspects of your posture and relieve stress on upper arm, shoulder, back, and neck. Try a split keyboard with some flexible supports (the ErgoPro uses the same kind of tripod mount as any camera) that allow you to adjust the two sides’ position independently, as well as all three axes of rotation for each side.
If you switch to a substantially different layout such as the TECK, Ergodox, Kinesis Advantage, or whatever custom keyboard, there will be an adjustment period lasting anywhere from a week to a couple months, depending. Standard ANSI/QWERTY layout is in many ways stupid, but it does have the benefit that you already learned it.
As hoggy said, this being Geekhack, nobody is going to discourage you from going as far down the rabbit hole as you like to go. We’ll happily cheer as you design your own keyboard layout, desolder all the switches from donor boards bought on ebay, cast your own specially shaped keycaps, etch your own pcb, and mill the keyboard case out of a block of aluminum using a hand mill. (Note: that’s what kurplop did, and the results are amazing.) If you want to get really fancy, you can follow that up by programming your own new keyboard firmware, or writing your own algorithm to optimize the logical letter layout.
One last bit of advice: if you post pictures, people will have an easier time giving concrete advice.
In any event, welcome to Geekhack, and all the best luck. RSI is no joke; stay safe out there.