The select neutral message is there to tell you you have tried to select a drive gear whilst the transfer box is still changing ratio and you should wait until the ratio change is completed...
The Ratio position is monitored by a set of 4(?) switches built into the transfer motor that give different open/close signals depending on its position.
When you changed the motor, I assume to lined it up correctly (read RAVE as I am not sure how that is done) so the motor, ECU and box all know where they are....
Also it is not uncommon for the wiring to break or the plugs to get cruddy giving a wrong position (or no position) signal to the ECU....
If you are getting the message yet still have drive, my thoughts would be to the position of the TB motor or crap in the wiring.