Experiencing lower abdomen pain, lower back pain, on my right side & missed period. Also just discovered a cyst on my right lower neck region. Related?

Probably not. However, a missed period with lower abdominal pain may be a sign of an ectopic pregnancy, which is a pregnancy in the Fallopian tube instead of in the uterus. You should be checked out, especially if the pain is getting worse - then you need to go to the emergency room.
Unrelated. UTI,Ovarian cyst,Endometriosis,Constipation, Indigestion, Appendix related and Diverticular disease are some of the reason for Abdominal pain. Muscle strain also contributes to Back pain. Cyst in neck region is unrelated.
Unlikely. It is unlikely that the cyst on your neck is related to the other symptoms. The other symptoms could be associated with a bladder infection, a pelvic imfection, appendicitis or a tubal pregnancy. See a doctor.