In reply to mikedelderfield:
Sorry, I posted without properly reading your op.
> 5. My right hamstrings feel pretty tight and a bit strained most of the time. They feel hyper fragile.
Gentle stretching really should sort that out if you keep at it, you might try flexing the knee while you're at your desk as well, like while you're sitting down gently extending your lower leg while your upper leg is static till your leg is straight. You could set a timer and do 20 every hour or something
> 6. My right achilles is also a little tender.
Definitely get onto the eccentric heel dips for that, if you can build up to being able to do three sets of 40 with no weight on each leg it should put you in good stead for avoiding any achiles related nastiness.
> 7. My right leg is 1/2 inch shorter than the left.
Do your hips dip if you lift your right leg of the ground?
> 8. I have been using orthotics for the last 6 weeks with no effect.
Make sure you ask the physio to prove why you need them, i.e. make sure they aren't just giving you them because that's what everyone does these days. Why specifically do you need them? And don't just take flat feet for an answer, why have you got flat feet in the first place?
> 9. Physio number (Private) one diagnosed a tight ITB causing biceps femoris tendonitis. She put me on a course of ITB & glute strenthening & stretches, along with ultrasound on the ITB & then bicep femoris tendon. This had little/no effect.
How long did you continue your exercises for? Some people seem to take a couple of weeks doing one excercise and everything is fine. Others take longer.
> 10. I haven't run for the last seven months.
If you can run for any more than 10 mins without pain then do as much as you can. If you've had a knee problem or you've been running off and on it will take a while for your legs to adapt to the stress again so the more gentle running you can do the better. I'm told that the body needs to "remember" how to run as well as just being strong/flexible enough to do it so the more pain free running you can do the better. Not just better for getting your leg back into shape but when you find your pain reducing you don't want your body's running ability to be at ground zero, having a body unused to running and the fresh motivation that comes from losing a long injury is probably a recipe for getting injured again!
> 11. Current physio (NHS) suspects some nerve snagging/shortening. So I am doing some stretches to try to correct this, though I am not convinced.
Buy the book "running well" by S. Murphey and S. Connors, it's the only running book I've read that actually touches on nerve mobilisation.
> 16. I have a desk job.
The guy at strengthrunning.com seems to stress how hard it is on your body to do a desk job and then expect it to play in the evenings and the weekends. There's some video's on there that are definitely worth a watch.
> What do you think am I doomed....doomed?
You're definitely not doomed! If you need to get your mojo back and find some inspiration read feet in the clouds, read it's not about the bike, Karen Darke's book, anything you can find where someones done something amazing with a broken body! Like a few others have said it sounds like your obvious weakness is flexibility so stretch like mad for the next few months and expect it to take time to get better but you can't doubt it will get better. If the doc/physios don't find anything wrong and in 3-6 months time you have a strong and flexible lower body then how could there possibly be anything that wont be better?
Ben