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I would not back the nut off to align the nut with the cotter pinhole. Doing so can result in the taper between the knuckle and the tierod becoming loose. The cotter pin would keep the nut from backing off but it would not prevent the tapered shaft of the tierod from spinning in the tapered hole of the knuckle. As @MikeSaull has suggested lube the threads. ...

I would use some anti-seize on the threads then tighten it to torque spec. If it doesn't line up then I would tighten it until it does. This is just what I would do. If it is a weak bolt or a really bad place for the threads to strip then I would just loosen it until it lines up. Once the cotter pin is in it shouldn't go anywhere anyways.