In an attempt to pay it back/forward, this post is for reference for those who are trying to replace the neoprene seals that go between the roof rack rails and the roof.

After a lot of frustration with the dealer and because they are "dealer only" parts, I found the following part numbers:

CAJ000040
CAJ000050
CAJ000020 x 2

However, if you dont want to pay $16 each, simply buy a 12"x12", 1/4" thick neoprene sheet, single side adhesive off of ebay for $6 and cut your own.

With any luck, this plus all the other stuff I did will stop all of my leaky roof problems, and will help those looking to do the same.