If the cotter pin hole isn't positioned properly then it's probably an aftermarket part manufacturing issue or the wrong castle nut was included in the kit. Does the original castle nut work better? If so, use that instead. If the OP decides to stick with the part then I would prioritize torquing the nut to the proper tightness above lining up the cotter pin. That pin is just a fail-safe to keep the nut from unexpectedly loosening. Not all steering and suspension parts use cotter pins. Some use lock nuts or thread-locking compounds. If the OP has threadlocker then I would suggest using that and putting the cotter pin in anyway, even if it's not positioned how it should be. Ball joints usually use an M10 or M12 shaft and castle nuts aren't typically very tight. The tie rod castle nut spec for this car is 33 ft-lbs (for comparison, the oil pan drain plug is 25 ft-lbs). I would personally tighten the castle nut slightly rather than loosen to align the cotter pin hole, just my opinion.
If aftermarket tie rod was used, I would again suggest getting a wheel alignment since even if the OP did a good job of marking the jam nut etc. there's no guarantee that toe will be as it was before the tie rod was replaced.