fingernails - low keratin, possibly either low blood calcium or low cysteine.
menstrual cycles - fix adrenals and watch for them to improve?
I don't know what alkaline phosphatase is

:
low GABA is associated with high calcium/copper, so high might be the opposite?
bowel tolerance SA happens when unabsorbed SA meets bacteria in the lower GI (large intestine? colon?) maybe you're not absorbing it well? Maybe your bacteria aren't in the right place? You're going by watery diarrhea tolerance, right? Not just gas?
There's a link between pain and prostaglandins
osteopenia - low blood calcium and/or low K2
vit A will decrease blood calcium
fidgeting - high dopamine?
detoxing antibiotics - acetylation (coA - B5, mag, cysteine (mag/b6))
BH4 - doubt it's low, cause of normal dopamine and thyroid, low serotonin is probably something else. Which means if there's a MTHFR issue, it's probably on the methyl side. Metals can block the folate/b12 path. betaine?
B6
gut bacteria - GAPS
metals
tests I'm curious about:
homocysteine/midline defects
blood calcium