Gav, the CDL switch is present on some, absent on others. This means it plays no part in stopping the CDL working so you can eliminate that. Same goes for the switch in the gearbox when in 'L' so it's not that, unless it's both at the same time, which can only really be wiring or the controller or the actuator. You've proven the motoring side of the actuator by jumping it and when it's in the lights come on and the other lockers work so you've proven its internal switches too. So that leaves control box and wiring. If you've changed the control box FOR A KNOWN WORKING UNIT from a working truck, then all you are left with is wiring.
Time to get the multimeter out (on ohms or continuity tone) and with an assistant, trace wire colours between actuator and control box/CDL switch/gearbox switch and do a diagram as you go to tick off each one in turn as you verify their continuity with the meter. One caveat is that sometimes wires go to more than one place but that should become obvious once you get stuck in.
Look for damage to wiring underneath, corrosion or missing/broken pins in connectors, or any sign of repair to the wiring.
Good luck with it.