The relay you are talking about is the AC control unit - its connected to the evap thermostat, ignition, blower switch, A/C rpm signal and engine rpm signal - the a/c rpm signal is sourced from the compressor rpm sensor itself and the engine rpm signal is sourced from the pump rpm at the back of the pump reading off the fuel limiting governor.
If the wires are not in place you will face problems - like the A/C compressor becoming gunked up.