Brake and turn signal functions pass through the multifunction switch, as does the cruise control. I would have to find the specific portion of the schematic to check to see if the running lights also pass through that switch. Regardless, you need to check the malfunctioning circuits and see what's going on. Is it loss of ground, power on the ground wire, low voltage on the the supply to the lights, something in the CC harness back feeding or shorting when it is connected? A multimeter and a schematic are your way forward. You should be able to find an electrical schematic for your truck on this site.