The stomach cramping might be anxiety, it's hard to believe a stomach is otherwise affected by bleeding from the vagina.
Please see your gyn again and at least get some hormone tests and a decent pelvic exam. If he or she can't think of an answer, ask for a referral to someone else, possibly a dermatologist or an endocrinologist.
Would your ob have noticed pregnancy if it was early? Only if you took a test. Would he or she have noticed genital warts or lichen schlerosus? Depends on how carefully he or she was examining you. Theoretically during a pelvic, the doc will feel your vagina with his or her finger (with the thin exam glove on) and theoretically any roughness of the skin or stiffness would be noticeable even through an exam glove. But it kind of sounds like your doctor didn't do a very thorough job trying to figure out what is wrong. Fact is, you have unexplained bleeding, and a good doctor will go as far as it takes in examining you and swabbing, etc. until he or she can come up with a diagnosis.