I am not following your description of the problem with the marks. If it were me I would take the tie rod ends lose and turn the steering wheel lock to lock and make sure rack had full range and the steering wheel was centered where it needed to be. Obviously the splines need to be locked but not beyond the realm to drill the clamp and use a larger graded bolt with a nut to get the required squeeze of the clamp. After verifying the foregoing then square-up/align wheels and see if the tie rod ends can fit as required. This could reveal a bent spindle.
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