Pain in lower right abdomen...again?

2 weeks ago, I started having horrifying pain in my lower abdomen, accompanied by heavy vaginal bleeding (after my period was a week late). I waited 3 days before going to the hospital, when the pain became too unbearable. They ran every test possible, blood, urine, internal and external ultrasounds, cat scan, internal exam, pap smear and colonoscopy (I have Crohns disease, and they wanted to look and be sure it wasn't that). He suspected appendicitis due to the location of the pain, but I had no sign of infection in my blood nor signs of problems with my appendix on the scans. The doctor was a bit baffled, as not only did nothing look wrong, but all my tests showed I was in fact in excellent health. He said it may have been something called a chemical pregnancy, where I miscarried before it even had a chance to attach itself, but that was his only possible reason for the pain and bleeding. It subsided by that Sunday, and I felt fine last week. This morning, the pain returned in the same area, just as intense as before, and came out of the blue again (no bleeding this time though). This time, however, if I lay flat on my back, you can feel a very swollen something (I'm guessing a lymph node?) on the lower right side near my hip. It is beyond painful to touch. My breasts have also become so sore it hurts when the rub against my bra or shirt. I'm am now 99.999999% sure this has to be something to do with hormones or my female parts. I have had ovarian cysts before that have ruptured and caused similar pain and funny female problems, but in the hospital, they saw no sign of them when the did the ultrasounds. Before I go back and look like a hypochondriac after being told I was in perfect health 2 weeks ago, what might be going on? Anyone have similar symptoms? I'm looking for things to suggest my doctor look for. I'm well in tune with my body, and there is something very wrong, even if it's hiding from the standard tests.