Persistent knee / shin pain

Shortened (as much as possible) history:

2004 - start running (10k training, ~15-20mpw)

2005 - start getting shin pain noticeable after running

Dec 2005 - something "gave" in right leg during 30 min run, tingling and twitching started

Feb 2006 - same symptoms in left leg (not as strong), gave up running (started spin classes, rowing, biking etc).

Summer 2006 - symptoms still present, bone scan ruled out fracture

2007 - still get strange tingling sensation in shins, pain starts to move to right foot (have done no running since Feb 2006)

2007 - knee pain starts, get x-ray, no serious problems but "joint connecting femur and tibia was quite shallow)"

2008 - still pain in feet, shins, knees (numbness, tingling in shins / feet, pain when bending knee (going down stairs)). Still no running since Feb 2006

2009 - no twitching, but tingling sensation still present. Try out some 10k runs, makes symptoms worse for a few days afterwards (shin pain, knee pain, tinging)

Jan 2009 - After particularly bad xmas, get a sports massage which seems to help with knee / leg pain and get referred to orthotist

Feb 2009 - Get custom orthotics to raise inside of my feet (diagnosed as having forefoot varus) causing twisting motion when lifting right foot. Seem to have little effect.

Aug 2009 -

See another physio, who says running style affected by right leg shorter than left (had been diagnosed by several people before) due to very tight quads, hams, pelvis misalignment. Go through stretching exercises to loosen all leg muscles and then pelvis is realigned succesfully(my right leg is now the same length)

Also notices that right calf is noticeably smaller than left - suggests that it's a result of my right leg not striking the floor properly and the calf not being used properly, so has atrophied. Calf is also very tight (feels like it has golf balls in it)

Also begins process of stripping scar tissue from right shin (inside of shin feels like a gravel track) using deep tissue massage. Seems to have a slight effect on the amount of tingling I feel after running.


Now - running occasionally and gym 3 times a week (spin, classes), but after-effects of running (knee pain, shin sensation) mean I don't do very much. Am doing calf raises to try to strengthen the right calf, icing of knee to reduce any inflammation, but pain and sensation is still continual.


Questions:

Does the leg length difference explain the calf atrophy, tightness? Is there an easy way to strip away the shin scar tissue, will continual massage work? Should this reduce the knee and shin pain, is there something else that could be wrong?

Is knee pain likely caused by imbalance in muscle strengths (a weak calf muscle would be unable to absorb the impact so would go straight to the knee?)

Any other suggestions / similar threads / tips?