Given his preserved mental function I would say he had ALS. ALS is a motor neuron disease. Chronic head trauma will affect cerebral function at a high level, where ALS will not.
From all the information I've seen Lou Gehrig did have ALS. There is a straight forward distinction between the two entities as ALS spares cognitive, oculomotor, sensory, and autonomic functions and chronic concussive syndrome does not.
Mohammed Ali has chronic concussive syndrome, Stephen Hawking has ALS. The two are quite different in presentation.
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