Hang on, before you go ripping apart a lower unit.
Are you positive that the shift control unit is the correct one for the motor?
Some motors go into forward gear when the cable is (shortened) by the action of the shifter unit and some when the cable is (lengthened).
If you are having to put the control unit in "reverse" to get the motor to shift into forward MY FIRST ASSUMPTION would be that someone replaced the original control unit with something off Flea Bay or something that was laying around cheap on the bench at a local marina.
You kinda make it sound like you were working on the motor to correct this issue and NOT the motor was shifting perfectly, and after you made some small change or adjustment it suddenly started it's "backward" operation.
So perhaps you could clarify before going any further - has this been the way it was shifting "since you got it"?
If so, then again, I suspect the control unit itself - might be able to reverse the cam of the "control unit", it has a cam too (some models can be reversed to fit multiple models) to change the cable direction - if not, then you have live with it (as the previous owner did) or replace the shift control unit - not the motors fault.
