I feel your pain :-( but on the bright side :-) I am currently correcting a lot of the same similar issues and after much frustration, i'm making good progress with it.
First of all, it would be handy to find a good physiotherapist or chiro. I couldn't and got frustrated and just started studying. I don't know what constitutes a good one, but if you can get someone who can prove that they still study and research the area, even after they 'qualified' then that would be a good start.
It sounds like you have alot of postural / balance issues. Weak glutes are a big factor and you will need to strengthen them and do some 'activation' drills which is - as far as i know- a way of 'reprogramming' your CNS to tell your glutes to fire when there supposed to. Basically, your body will have a lot of muscles doing too much work (for example, quads and hip flexors) due to other muscles not doing there job correctly (for example, glutes not firing, so the quads etc take the load).
You will have lots of weak muscles and effectively lots of other muscles compensating for the weaker ones, and therefore becoming over used / tight.
- if you've not been on this site get on it :-) Lots of great info. All the coaches / writers are good but Eric Cressey and Mike robertson have written loads of info on posture, function, mobility, inbalance - what ever way u want to put it, but it's all the same really - Functional strength i.e. strong but healthy.
The first thing I would very strongly advise you do is take a atleast 2 hours of your spare time ASAP and go through this article series, Neanderthal No More by Eric Cressey and Mike Robertson mentioned above. If you do anything, make sure you do this. 2 hours atleast, get your studying head on, get some paper and pen (or PC), get a camera and get down to business.
The article is a progressive series of which it firstly explains all the techical stuff which might be quite heavy going, but then it basically shows you how to diagnose your issues. You need pictures, and you are told what to look for and given info on how to correct it. At the very least, it will point you in the right direction and you will atleast have half a clue of what you need to do but I honestly believe that if you spend enough time going over these and maybe some of the other stuff they have written (check there own websites) then you will be able to figure it out your self.
here they are, in the order they were written,
http://www.t-nation.com/findArticle.do? ... 4-training
http://www.t-nation.com/findArticle.do? ... 6-training
Enjoy! Take it all seriously, i'm also a 'desk jockey'. It's likely that you have a string of upper body imbalances as well i.e. forward head posture, rounded shoulders, winged shoulder blades - a recipe for some chronic shoulder issues.
Sorry for the long (and a little rushed) post but it's a subject i've became very passionate about - I had no idea that this side of things even existed until I was 'out the game' for several months because of it.