I doubt a new rod would be bent or threaded off center, It sounds like the problem must be in the extractor. I have never tried straightening one. If you have a new (straight) rod, I'm not sure I would try to bend it to compensate for a problem in the extractor. I would replace the extractor.

Do you have another gun (same frame size) you could borrow the extractor from to see if it works with the new rod? That would isolate the source of the problem.