I lucked out: I was able to get my roof rack off without spinning nutserts or too much drama. I did have to replace a couple M5 (5mm x 0.8) nutserts. Many many folks have lots of drama just getting the port-installed rack off. The rust under my rack and wind deflector was essentially the only rust on my rig. My LC spent most of first 2 lives in Florida and Mississippi as a mall runner. Best to avoid pulling crack whore panties...
I got my hardware at a excellent brick/mortar store here in San Diego called Marshalls, but Bolt Depot has much of this stuff online (I have good luck with them in the past). The hardware I ended up using was (links give good images):
To hold down
roof rails (retained on LC): metric socket flat head, stainless, 5mm x 0.8, 25mm long
Metric socket flat head, Stainless steel 18-8, 5mm x 0.8mm x 25mm - Bolt Depot
To fill
roof rack pad nutserts: metric socket button head, stainless, 5mm x 0.8, 10 mm long
Metric socket button head, Stainless steel 18-8, 5mm x 0.8mm x 10mm - Bolt Depot
Sealing washers: M5 or close equivalent. This link gives you a good idea...
Sealing Washers from Estco Enterprises
Finish Washers (half-donut): I purchased, but did not (as yet) use M5 stainless finish washers. These (link below) are close to what I used (not sure if #8 is correct for standard close equivalent)...
Finishing washers, Stainless steel 18-8, #8 - Bolt Depot
I do not have data on the flat rubber washers I purchased for for finish washers. They are a tough, almost fibrous rubber.
I used the Loctite 565 as a thread sealer on the hardware, and Permathane as a painted steel-compatible sealer for the everything else. I am wary of using most silicone sealers as some release acetic acid as they cure, and most do not state they are specifically compatible with painted steel. I made a mistake with a silicone sealer on another car, and ended up with major rust.
HTH, Jon