Mice and keyboards can be a real pain -literally.

Getting your forearm, wrist and hand at the right angle, height and position is not easy, and on some desks is completely impossible.
something to try is a laptop 'tea tray' (the sort of thing you put on your lap to eat your chips whilst you watch the footie)  as a mouse-mat, it's a cheap option which can often help.
Another thing if you can't splash out too much cash is to get a similar object with a solid base, (even a bit of MDF) and a cheap camera tripod - drill a hole in the middle of the board, do some surgery to fix the camera screwthread to it. and you have a customised mouse mat which will work at any angle or height.
It will take a bit of extra work to get it so your wrist can rest, but it's not going to bust the bank (pick one up at a car boot sale if necessary)

Ergonomic keyboards are a must.  I know a lot of people don't like them, but they really help.
I absolutely loathe the standard straight things - we are just not designed to use them.

The choice of rat is also important.  get a decent sized mouse, trackball or whatever that fits YOU - spend £50 on it if you need to, but don't sacrifice your health for a miniature rat that you can't use.

I'm using a wireless keyboard and rat setup at the minute - that's because I now have to use a plasma display for my screen after a car crash messed my neck up, and a wireless system is great for sitting on the sofa working.

It's a Microsoft ergonomic kit.  Laser 5000 mouse and a fancy keyboard with it.
The ergonomics of the keyboard are good - but htis is one area that microsoft actually gets right.  If only they could produce software as good!
The mouse is slightly larger than some others, and fits my hand quite well.

Also look at some other input devces.  There are vertical mice around, and I can recall seeing a 3D input tool (a sort of 6 dimensional rat) advertised in 3D World.

Best advice (make sure you check with yourdoctor) is for frequent rests, Ice on the affected part, and good nutrition - you ain't gonna heal if you ain't eating properly.

Gentle exercise, and massage the muscles if you can't get toa therapist (there's enough info around the net to find which muscles control these tendons - go look!)
combine that with whatever sort of hardware setup you can afford, and you won't go far wrong.