The PDB (Power Distribution Board) that's the bottom of the quad provides power to everything. Battery power should go directly to the 4 motors and there is a voltage regulator on the PDB between where the cc3d mounts and the camera that regulates it down for the rest. Power for the cc3d goes into it through it's 8 pin cable to the PDB. The receiver could get it's power a couple of ways, I wired mine to get it from the cc3d's other 8 pin connector. Camera and video transmitter get power direct from the PDB.
Are you still running the OpenPilot software that came on it or have you upgraded it to LibrePilot?
jdn181 makes a good point, when you reloaded the software and ran through the vehicle setup wizard you said it all worked fine except the motors didn't spin. So all the input stuff worked but the motors never spun up during that part of the wizard?
Just to eliminate configuration errors you might post a copy of your uav config file. With the cc3d hooked up to USB go to file -> export uav settings. Attach it to your next post. That gives us all your settings at once.