Sorry to hear you have pain and nausea ... I'm in the same boat as you. I've had these symptoms along with bowel "issues" for 6 years now and after exhaustive testing, including a laparoscopy where they found endometriosis, I've been given the IBS diagnosis which I also question. Pain is my worst symptom and I have been on and off amitriptyline for it. I also get alot of right sided pain right over where the appendix is, do you also?
Sounds like your doctor did all the right tests to screen serious ailments out. Not sure if you know this or not but a laparoscopy is the only way to diagnose endo and then they can remove it (it can grow back ) and give you drugs to treat it.
Good luck and hope you find an answer soon.