*I have no idea if this is the correct forum. It doesn't really feel like 'tech'...

So, I like the sleek look of the truck with no roof rack on it. I want to be able to put it back on in the future for road trips, camping trips, etc. I took it off, and now see what's underneath. I'm going to paint my truck, so prep, sanding, body work etc. It leaves me with 2 questions.

1. Should I put something in these screw holes to plug them? For standard truck use I mean. I think i plan on putting the screws back in them during painting to keep the holes from filling.

2. If I take off the padding stuff, will i be able to use the rack later? Maybe by installing the padding on the underside of the rack instead of on the roof?

 

My WJ has inserts that fill the roof rack channels between the mounts. I'd need to buy full sections rather then the short pieces that fill the sections where the rack doesn't mount, but you should be able to find pieces that fit. Mine appear to be metal and are painted the same body color as the rest of the truck.

 

To my knowledge the padding just keeps the roof rack from rattling and rubbing against the paint. I see no reason why you couldn't attach it to the rack itself.
As for those holes, I would keep the bolts in and use some rubber gaskets as well. That will prevent any leaks. If you don't want the bolts to stick out you could paint them to match the body.