As a machinist that recently fitted a barrel it is amazing to me that many of the original barrels were timed so accurately that they could be interchanged. Perhaps the original was one that was off slightly or maybe modified.
The previous owner may have not tightened the barrel fully and used Loctite to keep it from moving? if so it may headspace a little large when you index marks and extractor cut line up.
Possible fixes, enlarge the extractor groove till it lines up and install aftermarket sights or get a new barrel fitted. If there is something off on the receiver a regular timed barrel may not interchange.
The barrel tightens against the end on the internal shoulder in the receiver, chasing an additional thread on the barrel and facing off almost .1 inch could make things work again with the sights lining up. The taper on the barrel is minimal, this would add slightly to the metal wood clearance but maybe not enough to notice. The extractor notch will have to bee deepened if you do this.
Check the head space as who knows now if it was correct with the barrel loose or tight.