You don't have to remove both cables, just one. I would suggest the ground cable, primarily because using a wrench to unscrew/screw it on, the wrench may touch a body panel or something metal on the truck. The body is connected to ground, so you get no spark doing the ground cable. You would get a spark doing this, if you remove the power cable first.
The switches you don't need to program. The module at the rear is programmed to the vehicle. There is also a relay (at least there is on my '12) mounted next to the module, which doesn't need programming when it is replaced.
The silicon I mentioned is a solid gasket, that is part of the connector that is on the truck's harness (and not something like rtv that is applied to anything). It's like a thick, soft rubber seal that keeps out dirt and moisture from the connector when it's plugged in. If, when you are installing the connector onto the module after it's mounted on the truck, and it feels like you need to apply too much force to the lever, pull the connector off again, and lube that silicon gasket with some dielectric grease (I used a qtip to do this, as the gasket is down inside the connector a bit), then try instaling it again.