Magnesium malate is good to dissolve stones due to malic acid, which is found in apples and cranberries.
Mag Glycinate is *probably* better for absorbing magnesium, but you never know until you try.
I think another thing to try is Epsom Salt baths. Get a giant box of it, dump it in warm bath and soak for a while.
As far as flukes go, it's just a guess. But with that amount of congestion it is likely that some parasites are in the mix.
You might just have a pinched nerve, which can be excruciating, but it's better than nerve damage. Pain on either side of the neck is related to liver congestion. I would try to get some manual therapy done like norway massage, it's better than swedish massage.
Vata/kapha is a difficult combination. The common elements are non-pungent spices, and not too much else since they are opposites. Maybe plain rice. Look into 'tri-doshic' food choices. It sounds like you are vata dominant, so try the vata pacifying diet first. There are a lot of websites describing it in detail.