In my limted experience it seems that in flushing the smaller, younger stones pop out and that in subsequent flushes , older, larger, gnarly looking stones come out. My first flushes were like yours (bright green electric balls) but later on I got larger, tan stones that looked ready to be petrified.
As for the skin issues, I think thaht after your parasite clease you had a lot of parasite toxins trapped in your skin where they surfaced because the other pathways of detox were clogged. Now that your bowels and liver are cleaner I suspect the skin issues will subside.
However, remember to start another parasite program in a few weeks to keep you supply of pets LOW.