Ha Ha
No, didn't end up getting stuck! I forgot about this thread, though. It does need some resolution, so here goes...
Bottom line:
The 3M 5200 Marine sealer is awesome. It took about 5 days to dry, but the leaking problem is completely fixed.
My how-to:
There were four cracks in the roof where the water was getting in. Three of them were where the sheet metal comes together under the roof rack feet. The other was a similar crack just left of the drivers side liftgate hinge. I didn't need to remove the headliner to fix them, because I sealed the cracks in the sheet metal seams from above.
It's not too hard to remove the side roof rails. The black plastic covers on either end are held on by the same metal clips that hold the plastic interior trim pieces on, and if you pull up on them, they should disengage. I used a trim tool to get the necessary leverage, but I bet a large screwdriver will do.
Once the end cap is off, there are two dome-shaped nuts that hold the roof rail on. These can easily be removed using a ratchet and the right sized socket. There are two nuts for each end of the roof rail.
Once all nuts are off, you can lift the roof rail off the Jeep. There will be some clear rubbery sealant between the roof and the rail, but this should separate from the rail as you take it off.
I found that the factory did a terrible job at applying that sealant, and it missed some places entirely. Under the sealant is where my roof had cracks. So I painstakingly removed the old sealant (which is not easy and hurts your fingers!). The best method is to stretch it sideways/lengthwise so it slowly disengages from the paint. If you try to pull directly up on it, some of the paint will come off with it along those cracks.
Once I had the old sealant off, I cleaned the area, then liberally applied the 3M sealant to the entire area under the roof rack feet, essentially creating a rubber mat between the vehicle and where the roof rack feet go. I waited for everything to dry (several days) before putting the roof rack rails back on, because I didn't want to permanently glue them to the vehicle.
I also sealed the entire seam that goes along the top of the rear hatch, above the gate weatherstripping and below the roof. I had some serious rust in this area (including a 1-inch crack where two pieces of sheet metal came together, just left of the drivers side gate hinge). I completely covered all of the rust up with the 3M sealer, filling the gaps and protecting against water intrusion and future rust. It isn't pretty but it's effective. And it is all hidden when the trunk is closed.
Another couple of tips:
The sealant is black in color and has the consistency of roof tar or chocolate cake batter. I used a disposable plastic spatula (like the kind you could use to spackel drywall) that I picked up at the hardware store for $0.99 to spread and smooth the 3M sealer. It's nasty stuff and you don't want to get it on your hands.
The water stains on the headliner cleaned right up using Dr. Bronner's Sal Suds (sort of an organic soap/cleanser) and water. I got >90% of the water stains out using this and a wash cloth.
Good luck!
Lauren
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2008 Liberty Sport 4x4 Automatic
Jeepin By Al 4" Lift Kit
BFG KO2’s 245/75R16
Full MOPAR skid plates
Rock Lizard Skink Super Sliders
AtTheHelm Front Recovery System & Roof RackM116A3 Trailer build thread: viewtopic.php?f=72&t=77997