Slide your housings out of the slotted stops (plenty of videos on YouTube- might as well lube the, up while you have access) and inspect the cables themselves, sometimes a kink in the cable can do this. The kink usually comes from the bike being bumped or packed weird among other bikes in a car or on a bike rack.

For the record, you can set the limit screws pretty close to perfect without the cable (do this with the cable detatched or the housings out of the stops) at all- push the RD with your thumb through the range and adjust the limits to where you can just make it not the high and low.

Also, eyeball the RD hanger alignment, a bend can dramatically impact indexing.