Some of what you mention, desk job, carpal tunnel, neck,shoulder, back pain...and the headaches, might be related to Thoracic outlet syndrome... TOS for short..
Here is our TOS forum useful sticky thread , you may find some helpful information..even if you don't have full blown TOS the tips & info in all the sticky threads there is beneficial.
http://neurotalk.psychcentral.com/thread84.html

You might benefit from an expert PT evaluation, or even expert chiropractor if you are open to that.
Soft tissue tension & muscle spasms can cause many issues.. headache is one.

But a MRI of head & C spine is usually done , just to rule in/out any possible spinal issues or internal brain issues. Also a vision/eye check is a good idea..

If GP isn't following up as you would like, I'd find another GP...