I agree with hopinso that it is probably die off reaction and to keep an eye on him.
Also be sure that he is drinking plenty of water to flush those toxins out of his system and to be getting extra rest.
When the body is overwhelmed by the dead and dying parasites and all of the toxins created by such then it will need extra rest so as to put more energy into removing the toxins and healing.
Some vitamin C might help too as I have read that it helps neutralize toxins and get them out of the system. I am doing a cleanse now and am taking vitamin C to help with the toxins. I also make sure to drink plenty of fluids and try to get extra rest.
With the extra water, extra rst and vitamin c I don't seem to get any really nasty reactions from all of the die off.
I so seem to get headaches while cleansing but I believe it too is from die off (it is possible it is from the wormwood though as now that I think of it, it only happens when I am on the cleanse with the wormwood and not while using the grapefruit seed extract or zapping).
I do know that the wormwood is supposed to be a hormonal and it tends to make me spot bleed but seeing as how your son doesn't have a period that won't be a problem for him :-)
Keep an eye on him to be sure he gets extra rest and lots of water. The darker urine could be from not drinking enough water. If his symptoms get worse or don't improve then he may need to cut back on the cleanse, or take a break from it, and see a dr. Be sure that it is a naturiopath so that they will understand the cleansing process and what is happening.
Most regular drs are not taught about parasites and cleansing.