this thread is somewhat dead, but i wanted to post this in case anyone searches this problem in the future:
my leak turned out to be a pinhole in the caulking of the windshield. the diagnostic process went as follows:
1. TMS replaced all the seals on the roof rack, re-torqued, and ran it through their pressure washer. it leaked.
2. checked windshield. found small hole in caulking. resealed that area, still leaked.
3. dropped the headliner, checked with water and compressed air, found another pinhole in the caulking of the driver's side top corner of windshield. resealed, problem fixed.
some of the production engineers came to check it out, and they plan to follow-up at the factory in Japan to see if there is a flaw in the production line.
AND, i am sure that after all of this, i am going to get a rock to the windshield any moment now!!
