It could be the rear derailleur hanger is out of alignment.
Check to see that the rear derailleur mounting bolt is threaded completely into the hanger, and that it's not cross threaded or wonky.
I'll assume you know what the stroke adjust screws do, and how to fix the cable to the derailleur.
Sometimes you can get more accurate shifting if you trim the barrel adjuster when the chain is on a middle position cog- like 4/5/6 position- so the cumulative distance between 'adjustment point zero' isn;t as great at the ends of the derailleur movement range.
I hope that makes sense.
But yeah, it may be the deraulleur hanger is bent or the der cage is tweaked. There might be a missing spacer, but it would be pretty obvious- the cassette would not even be close to tight.