Hi there...
I've had both PCOS and endo. The main difference was with the endo I'd have really terrible heavy periods almost continuously. With PCOS my periods were very haphazard, non existent at times.
But the thing to remember is that everyone's condition will vary- so its hard to make the diagnosis. My hormone levels were always fine- except for insulin resistance- which is way off.
Maybe get a 2nd opinion- both my endo and polycystic ovaries were picked up on ultrasound scans.