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Seeking Diagnosis Direction for Juvenile Onset Dystonia, Spasticity and Clubfoot

I apologize for this being so long; however, my son has a complex medical history.

My 13 yr old son has developed dystonia, spasticity, and a clubfoot (left) over the past 3 years.  He was born premature at 36 weeks, had low blood sugar, and had difficulty with feeding and sleeping.  He was very "colicky" until he was 8 1/2 months old, but reached all of his 'physical' milestones timely.  He was obsessed with spinning objects, began to regress socially at age 2, and was very quiet throughout his toddler and preschool years.  He was diagnosed with mild/moderate infantile autism at age 6, and has all of the associated behaviors and symptoms.  He is verbal, but has difficulty recalling words and has a speech impediment, and he has sensory dysfunction for all senses.  He chews (usually paper) most of the time.  

My son has taken Lexapro to control self-injurious behaviors since he was 7, and Seroquel for anxiety and chronic insomnia since he was 11 1/2.  He was diagnosed with epilepsy 6 months after he was diagnosed with autism; however, his seizures are currently controlled with Lamictal.  He was diagnosed with spastic diplegia cerebral palsy 1 year ago.  My son performs at the 1st to 2nd grade level in reading and math, and his last IQ test, when he was 8, was 74.  

At age 4 he began complaining that his feet felt "hot-cold" (his term) at bedtime and would move them around a lot.  At about age 8 I started noticing that his feet felt stiff when I put on his shoes and socks.  At age 10 and 3 months I noticed his left leg would "bow-out" when he walked down stairs.  Shortly after he began to have severe episodes of what he said were "sparkly feet" at bedtime that would cause him to become distressed and his foot and leg muscles would cramp up.  (I could even hear his joints at his toes, ankles and knees pop.)  I began to notice when I checked on him as he slept that he was having muscle contractions - usually on the left, but sometimes on both sides - that would cause his legs to pull up into a "frog leg" position.

He began wearing shoe orthotics 2 years ago because the tendons in his feet and ankles were tightening and his left foot was rolling out.  Starting last summer, he began to get stiffer in his feet and legs and his left foot started to contract into a clubfoot position.  (His left calf is also smaller than the left.)  In November, an orthopedic surgeon examined him and diagnosed him with a clubfoot and shortened tendons on both sides.  (The orthopedic doctor was shocked that he was not born with a clubfoot or any orthopedic problems.)  His right foot is 1 1/2 inches longer now than the left; however, it is starting to roll-out like the left.

My son takes Tizanidine and receives Botox in both calves for the foot/leg stiffness, spasms and pain.  (Botox "A" every 3 months in both legs, and Botox "B" in the left leg every 3 months - alternately with the "A").  He continues to have muscle contractions throughout the night and day.  He is receiving physical therapy at school and one night a week.  We preceived a custom stroller (wheelchair type) for him last week, because he can only stand/walk for about 20-30 minutes before the pain in his feet is too great and he has to sit.  His left foot/ankle are casted to try and get them into a position so he can wear a leg brace.  He will have leg braces for both legs made, as soon as the left is in a better position.  His neurologist has also prescribed Tylenol with Codeine #4 for my son's pain.

His neurologist has done MRIs of his brain (normal except for polymicrogyria), his spine (normal), a head CT (normal) and x-rays of his legs and spine (normal) over the last two years.  He also ran preliminary tests for muscular dystrophy that were also negative.  My son also has had a few episodes of tachycardia the beginning of last year, but a cardiologist did an ultrasound and it was normal.  The neurologist referred us to a specialist to see if his night-time muscle cramps are seizure related: They are not.  

The seizure specialist referred us to a metabolic specialist who ran some tests, but seemed more interested in finding out if he has Prader-Willi Syndrome because of his medical history (low blood sugar, feeding problems).  My son is slightly over-weight due to reduced physical activity that resulted from the foot and leg pain, but he is not obsessed with eating.  In fact, he would never eat if we did not tell him it was meal time (it's an autism thing).  The metabolic tests he did were negative; however, he did mention to me that the tests showed that his bones were releasing something and he didn't know why.  (I can't remember what he said they are releasing.)  

The metabolic specialist said he wanted him to see a dermatologist and endocrinologist to help determine a direction to look into.  (He has some dark colored skin spots on his throat, dry itchy scalp, and has had a red rash on his upper back and coffee colored spots on his buttocks off and on for the past three years.)  The dermatologist said the skin issues were consistent with several different kinds of metabolic disorders, including diabetes.  My son had a complete endocrine work up last month.  All of these tests were normal; however, the endocrinologist commented that he has a large head and said he should be about 6'2" when he stops growing. The metabolic specialist is doing one final PWS test, then said he will release him back to his neurologist for ongoing care.  He does not know what is causing the dystonia, clubfoot, etc.

At his last neuroology check up, I reported that my son began having episodes two months ago where he blinks his eyes for 5-10 minutes and he has also been complaining that his arms hurt just below the elbow.  His neurologist said the eye blinking is a tic.  His neurologist also told me he thinks my son will continue to get worse in his legs, but does not think the problem will be as severe in his upper extremities.  He said outside of the treatments my son is already getting (and possibly a Baclofin Pump in the future), there is probably nothing more that can be done for him.  He is referring us to yet another pediatric neurology specialist, whom we will see in August, for more tests to - hopefully - help find a diagnosis.  My son's neurologist told me we may never have a diagnosis; however, I really need to know what to expect in the long term, so I can plan for my son.

My questions is: What condition(s) should the doctors be testing for - or to rule out?
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