Silas, first let me say that I'm sorry your son is going through this - I know it must be hard on you, as dad, to watch him be so uncomfortable. The treatment protocols are pretty basic.
Here's what I found on the web:
ETIOLOGY
The precise etiology of HaNDL is not yet fully understood. Though some initially speculated that the syndrome represented a severe migraine [4,5], others favored an inflammatory or infectious origin, given the CSF lymphocytosis, frequent viral prodrome, and monophasic course [1,2]. However, despite extensive viral serological evaluation, there are few reports confirming a viral association. In one early case, echovirus 30 was isolated using cell tissue cultures from a patient with an illness resembling HaNDL [6]. In another case of HaNDL, serologic evidence of human herpesvirus 6 infection was detected by an elevated titer of IgM at presentation that gradually decreased to normal range by four weeks after admission [7].
It does look like there is an infectious origin, and MMS is definitely good for that.
I would start with protocol 1000 (you can find it in Jim Humble's book, or you can find it on his website
www.jimhumble.biz) - and go from there. You may want to start with 1/2 drop an hour activated for 8 hours the first day, and if there's no problem, add another 1/2 drop the next day to 1 drop an hour.
Is your son in school or away from home part of the day? If so, you may want to use the (what I call) waterbottle technique - which Mark shows in the following YouTube video -