Differential - All input welcome!

The differential includes but is not limited to:

Shortness of breath worsening with exertion/exercise intolerance
Arthralgias
Myalgias
Spasms
Feet and ankle contortions
Nerve and muscle pain worst in lower extremities and increasing down the legs
General muscle weakness
20 + MRI lesions indicative of TIA strokes
Neurological symptoms of speech, memory, concentration, tingling, numbness
Intermittent debilitating fatigue / general tiredness
Degenerative Disc Disease
Need for Gall Bladder removal - elevated liver enzymes and possible jaundice appearing
Near toxic levels of Vitamin D in the absence of diet or supplement
Hypoglycemia
Asthma
Latex sensitivity increasing reaction with prolonged exposure
History of:
Anticardiolipin Antibody Syndrome
Allergic reaction to Adenosine Phosphate, seizure
PE, DVT (post operative)
Cervical Fusion
Normal EMG
Normal VEP
Normal Venous Doppler
Ruled Out almost all standard autoimmune diseases and then some including:
MS
Lupus
Sjogren's
Arthritis
B12 deficiency
Chronic Fatigue
Porphyria
Many others

Family history includes:
Mother who died at 66 with a necrotic stomach, chief admitting complaint - leg pain. Pattern of progression extremely similar. Also exhibited COPD, hypoglycemia
Grandfather deceased now, with early heart attack (40's) stroke (mid 50s to early 60s)
Father with hypothyroidism peripheral artery disease, treating with anticoagulants
Oldest Son with unidentified apparent syndrome. Presentaiton includes; bilateral cleft lip and palate, schizoaffective disorder, boney abnormalities, arthralgias and myalgias, exercise intolerance, type II diabetes, supernumerary thumb
Daughter beginning to exhibit increasing exercise intolerance, gall stones at 10 years of age requiring removal by 12
Youngest son diagnosed with Aarskog's Syndrome and Asperger's. History of reactive airway disease currently treating with maintenance medications and monitoring

Theories include:
Possible genetic connection
Metabolic/Endocrinological condition
Intermittent Anticardiolipin Antibody Syndrome aggravated by infection or inflammation (such as gall bladder) resulting in multiple TIAs, PEs and DVTs (venous has since returned normal for DVT, CT just completed)

Further tests scheduled include: Spiral Chest CT for PEs, Galium Scan.
Blood screening tests in progress for clotting, Lupus (again), Sjorgen’s (again), Mitochondrial Myopathy, Huntington’s, others

Any ideas at all on where to go with this?? Any best guess is appreciated. Also, I'm happy to answer any questions which might facilitate a differential. Thank you very much!