Kevin,
Sorry I did not reply sooner -- I was waiting to see if a leak that developed was due to the roof rack (it wasn't and turned out to be water getting under the carpet from the A/C duct opening through the floor, which the dealer resealed under warranty).
So now I feel more comfortable giving you advice ...
1. Just the holes -- I used regular clear RTV silicone to seal the holes, which I drilled only as big as needed for the bolts to fit in (I understand the factory holes are larger for ease of installation). The order of assembly is a bolt goes through the roof rack rail, a washer goes on the bolt between the rail and the roof, and the nut goes on the bolt on the inside of the roof; I applied silicone to each part (which also kept the bolts and washers together for placing the rack into the holes) and when tightening the nuts the excess squeezes out and you can wipe it off. Below is a reply from Permatex when I recently inquired about the best product to use when I thought I would have to re-seal my roof rack (which I fortunately did not). Note that I did not even think to use a threadlocker -- sounds like it would be good to add to your list.
"You can try using the Removable Grade Threadlocker 242 to lock and seal the fastener,then apply a Clear RTV Silicone #80050 or use the Permatex Flowable Silicone #81730 to seal around the holes. If you have additional questions you can call the Permatex Tech Center 1-866-564-8461."
2. Your suggested method (starter holes from inside, align the rack, then drill down through) might work better than what I did. When you look at the inside of the roof, while you can see the general spots for the rear holes and two of the side holes, it isn't that clear exactly where to drill (they aren't pre-stamped or anything) and the front couple of holes have no location indicators at all. So since I pre-arranged the purchase of my rack from someone who had not yet removed it, I had him take measurements from the outside. What I did was then line up the rack on top of the roof, sans bolts (it has foam padding on it so it won't scratch), taped it down with masking tape and just drilled the holes through the holes in the rack. I still have the measurements if you want them.
3. The headliner removal is not difficult, but is involved. There is a guide on ptdoityourself.net A nice tool to have, which is mentioned in the guide, is a trim stick which is plastic and won't scratch pieces you need to pry up. Getting it back on tight is not a problem as the sunroof, overhead console, door grab handles, door rubber trim and trim pieces hold it up in addition to two rear push fasteners.
Let me know if you need anything further.
Chuck.
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