One quick thing that I did not see mentioned. I had/have all the same difficulties you listed. I actually used many of the tips listed by xanadu00 to help make my PC experience better.

One thing that I did not see mentioned that may be worth experimenting. I had compact fluroscent lights throughout my house and was advised to get rid of them by my behavioral optometrist and switch to regular incadescent bulbs. It made a huge difference when watching TV or computer. Something in regards to the dip in the color spectrum (green if I recall) for those types of bulbs that your brain cannot compensate for properly. Trying to remember what I was told so it could be incorrect.

At work now where I have that awful commercial lighting, I just have a table lamp above my space with a regular bulb and it helps alot along with f.Lux and workrave mentioned.

Just a side note, I did 5 months of vision therapy. Had another injury which upset my eyes again and had to do 2 more months. It made a huge difference, I also now wear a pair of prism glasses at work for my computer. I still get some issues in very busy public places (Costco, etc...)

Good luck!