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Some issues I would include in the root cause analysis framework:

Known genetic anomalies: what is their mechanism?
What kills the cell and how?
Why does the disease seem to progress to neighboring cells instead of starting in different places separately?

Role of inflammation
Known clusters (including Guam)
Protein misfolding/sticking
Vesicular transport

Why is ALS more common in males?

Why does the disease affect motor neurons but leave sensory neurons mainly intact?

Other known cellular anomalies (faulty receptors etc.)
Known lab anomalies
Reports on remissions/reversal of symptoms

That's something to start with. Then proceed by sticking the research data in appropriate positions, adding new points as necessary. In the end, the pieces of the puzzle might start fitting together and the separate research results might start to make some sense.

All the while, it should of course be kept in mind that we are probably talking about several different diseases, but they all share some common things in any case.