I've been working on the roof-rack stuff quite a bit lately. There are at least 3 different styles of roof-rack from the factory. The side rails that hold the cross bars are put in with some rubber encased nuts that are set into holes drilled in the roof.
The earliest version (as we have on our 84) had the skid strips that screw into the roof with some (impossible to find) plastic runners under them. These are stainless steel with rubber strips in them. The next style they ran had the stick down skid strips that I think were still stainless. Then they went to a black stick-on style and eventually changed the side rails to the black as well with a push-button instead of the screw down mechanism they had early on for the cross-bars.
I think teamcherokee has a complete roof-rack available NOS if you were really interested, but I would seriously consider the aftermarket styles that will fit your needs. The look of the Jeep without the roof rack will grow on you if that's what you're concerned about