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What transmission has the tractor, Is it the full powershift?
Sorry for my late reply
I have been talking to an ex colleage of mine who is still working at a John Deere dealership. He suggested to check the wiring underneith the shifter, and hopefully you will find a loose connector or rubbed trough wiring, even follow the wiring on the outside of the cab.
If you don't find anything the JD dealership will have to hook it up to their laptop. I used to have the software, but since i quit at JD they took it of my laptop