Removing everything from the roof is a really simple job. Each roof rail has 4 or 5 torx screws holding it to the roof, the outer 2 torx screws also hold down a plastic cap preventing you from sliding the cross bars off. Once you remove the rail caps you can slide the cross bars off, it makes it easier to lift the roof rails (the ones that run the length of the roof) off. If the last owner hadn't put a hardened plug in one of the screws, I could remove everything off the roof in 15 minutes.

From there you can go about disassembling the roof components. The crossbars and roof rails have a rubber insert to protect the paint when they are fitted to the roof, you can just slide it out. You need a Philips screwdriver to separate the plastic part of the crossbar from the aluminum part (I'm only painting aluminum so I separate the plastic parts). I keep everything labeled in plastic bags, but I don't think there are any parts that could be mixed up.