Doing the parasite cleanse is supposed to help with nausea. With headaches, I find drinking alot of water during the day (during hours you can still eat) helps. I am prone to headaches, especially after Epsom Salts and this did help me. Shoulder pain sounds like gb related. To reduce gb pain with flush, I upped my oo to 3/4 c. instead of the 1/2 Dr. Clark says to use.
Good luck and don't give up. Even with the side effects, flushing is better than surgery!!! I was supposed to have surgery also because of multiple stones and frequent attacks. Now, here I am 5 flushes later (not done yet though) with all parts still intact!