It is best to keep the Pink wire of the GPS connected. The ECM reads the resistance value of the GPS, which varies according to the gear that is selected. In turn the ECM selects fueling based on the GPS values.
This link takes you to a diagram on SteveTLS' page showing the OEM configuration of the GPS.
Since the pink wire is already cut, this would be a good opportunity to install a 6.8K ohm resistor in series to produce a simple form of a TRE. This would eliminate the retarded timing built into the ECM in the first three gears.
See Steve's explanation at: