Best way to route wires from roof?

I have a 2011 4D Tacoma 4X4 TRD with the factory roof rack, the one that pivots across the roof when in the use position. At some point I want to get the Surco roof rack and permanently attach it. This means I would add the Surco lighting option, 2 lights, to the rack and I am a ham radio operator and will need to route these wires/cables to the inside. I might route them down the center pillion so I can place the radio under the drivers seat and light switches on the console.
Any advice on how to do this without causing leak or rust issues would be greatly appreciated.
Thanks in advance!

 

Route the wires from the roof into the cab thru the third tail light at the back of the cab.

 

If it was just an antenna, I'd say install an NMO mount.

Be careful when routing wires up there now--you have airbags in the roof. You don't want to run wires near or over those bags, especially antenna wires that could cause RFI.