They are hanging out about 4" at each corner. They come wrapped in a plastic bag which also contains a connector, so if you pull off the bags make sure not to throw them away, it is hard to see the connector in there.
You can tape up the wires with black electrical tape if you are going to install later, or if you are never going to install lights, then you can probably tuck them back in and seal the hole with a grommet or something.
The instructions for the light install are here:
Toyota FJ Cruiser: Resources & Documentation Archive You will need to order some spare clips. I need to do that also.
As far as the rack installation. It is pretty straightforward as shown in the instruction you linked. If you have a factory rack, you will needs some star-shape torque bits to remove that with a ratchet. The installation requires another person when you lift the stealth rack onto your vehicle, other than that it is simply putting some some bolts through the new plates that cover/go through the existing mounting receiver, bolting on the new Gobi brackets, lifting up and aligning the rack, and bolting it on before tightening everything up.