I would take the rod off of the trans horizontle flat shifter lever & move the lever to neutral then adj the shifter to the neutral position then shorten/lengthen the rod so it drops right down into the trans lever. or any other position of the trans lever & with the shifter in the corresponding position (park/park etc). that might be too simplified but that'd be my take/where I'd start. then see if each shifter position places the trans in the gear it is supposed to be in.
The adjustments are there for production cars, so make sure the rod drops into the shift lever in every position
Take your time and don't get frustrated, hopefully you'll nail it the first time