I did the exact same organic apple juice flush on my first try (assuming you did salt as well?)!
Then I switched to grapefruit juice and altered some other things.
Honestly, I don't know what the side pain is about. Hope it isn't something else. The only pain I had was across my back, between my shoulder blades.
It took 4 flushes before I had enough stones out that the pain went away.
I've gotten out ~1750 now - 8 flushes - they fill a small tupperware container. The most came out when I did a P&B shake 2 days before the flush - got 943 that I could count.
Epsom Salt always seems to help me with minor gallbladder related pain and indigestion. I put it in pills and take 2-3. Works when my bowels slow down a little, too...I'm doing P&B shakes 2x/day and parasite medicine now.
Hope this helps.
It's really worth it, getting all those stones out, even if I have to do follow up maintenance now and then! Don't give up! Lots of good people on here will help you (and some flakes that will leave you shaking your head)
I also recommend doing a little psyllium husk or something after a flush - P&B shakes are ideal. I discovered that a whole bunch of Gallstones left my gallbladder...only to get stuck in my colon like flies on flypaper! It caused me really stinky gas until I got them out.