When mouses were first appearing, there were some absolutely atrocious designs out there that gave no thought to the shape of the human hand, but over the years the shapes have 'sort of' standardized. On my '98 machine I have a digitizer pad and the 'nouse' is set up in one square inch in the middle of the pad--not good for really fine graphics, but great for normal use, when a slight flick sends your files flying to their new destination. For graphic work, I have to expand the field back to 1:1, but it's quick and easy to do.
Personal choice, trial and error, visit friends and try out their mouses; and yes, those micro-size things being touted for laptops--a complete pain in the arm, you thumb and ring/pinky fingers are doing so much extra work holding the damn thing whereas a full size mouse you can rest your hand and relax a little.
Keyboard: I tried a MS 'natural' for three months and absolutely hated it. The tactile feedback from the keys was woeful, and having those gargantuan space wasters between the CTRL and ALT keys just inviting you to bump them and get kicked out of your program was so frustrating I removed them. I went back to a TACTILE flat keyboard and was back up to 80+ wpm in minutes. If you really want an ergonomic keyboard for continuous keyboarding, look up Maltron in the UK. They're expensive, but worth it.
Lastly, DO NOT sit at your computer for hours on end. I suggest taking a walk around the office every fifteen minutes or so. That thirty seconds will make a huge difference to your work performance. When waiting for a file to save or load, do finger stretches and take your minimum FIVE minute break every hour. Your body wasn't dessigned to sit in a chair statically with your eyes glued to a radiation emitting screen and your hands stuck 3cm off the desk in front of you.
You need to get of that chair and move around, keep the blood flowing and your body will be thankful rather than keep fighting you; and as pointed out elsewhere, if you have significant problems consult a Doctor (sports medicine is the closest to dealing with RSI) or an Occupational Therapist.