L.R.
Yes, it could be endometriosis but you need to see a NEW doctor to diagnose you for that or anything else. Your doctor is lousy and not pursuing what sound like horrible symptoms.
Ask yourself: Does this affect my ability to lead a normal life? Yes, clearly it does. So please find a new doctor tomorrow and go in and be assertive -- insist that this makes your life unliveable and you will not leave until the doctor has scheduled procedures and tests to start finding SOME reason for this.
Please don't ever assume that something is a kidney infection or anything else-- and if it were indeed a kidney infection, you needed antibiotics, not over the counter meds. I really hope you find a good, aggressive doctor and are assertive with him or her. You do a good job of tracking your cycles and have all the dates of skipped periods, etc. -- take ALL that to the doctor. Tell the doctor you need extra time and expect to sit down and talk, not just have a five-minute exam and be dismissed. Something is wrong but your current doctor is ignoring you.