If you are sure the rods are correct and you didn't adjust any of them...now if the shifter is in natural as is the tranny..You should be able to see if the rod ends fit into the arms. If not adjust the arm on the shaft (keeping track where it was). There has to be some parts of the puzzle that you know are correct then the rest falls into place.

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1985 Euro 240D 5 spd 140K
1979 240D 5 spd, 40K on engine rebuild
1994 Dodge/Cummins, 5 spd, 121K
1964 Allice Chalmers D15 tractor
2014 Kubota L3800 tractor
1964 VW bug

"Lifes too short to drive a boring car"