I had hand/arm problems not long after starting my first programming job, but I have solved them now.
My main advice would be to get a good chair and desk. I have a RH logic 400 chair and height adjustable desk, with an Imprint Cumulus Pro floor mat. I also use a Kinesis Freestyle 2 keyboard. All together this cost about £1700, but it was absolutely worth it. I spend approx 50% of my time standing which I find much more comfortable than sitting.
My other piece of advice would be to take regular breaks. I recently became self employed which allows me to intermingle work with exercise, socialising and eating as I want. This really helps with fatigue. At least try to take a short break once an hour. I found jawbone up good for this as you can set it to vibrate after you have been sat idly for too long.
Finally, if using the mouse is a problem, learn to use your non-dominant hand. This has pretty much solved my problems with my mouse hand.