The biggest source for water inside my '97 Cadillac is at the sunroof. For some reason the thing just doesn't want to seal right, no matter if it looks it or not. The thing is, the water doesn't come in through the seals like you'd think, it actually flows underneath the inside lining along the roof interior, and ran back into my back seat. The only reason I noticed this is... well it's Georgia and it rains A LOT during the summer time. My seatbelt started to mildew because the rain water was soaking it from the inside... Still haven't fixed the problem on mine, but yours could be a similar case. It's very hard to see, until it's too late. That's my two cents.

 

...and that's probably because of clogged vinyl drain hoses. There is one running from each of the four corners of the AstroRoof to the four respective fender area and if one gets clogged or dislodged, water can and will go where ever it wants.

 

How can you find these roof drains. My 95 STS fill up under the rear seats way to much. Like 2 " or more.

 

most cars have floor drains with a rubber plugs.
pull the plugs and for now, let it drain.

i keep drains clear with a narrow stream nozzle on the hose,
the kind that that cannot be adjusted and only shoots a straight stream.
i shove it anywhere it looks like a drain and let it rip.

dirt, silt, mud, and leaves are all RUST magnets, even in CALIFORNIA.
that stuff gets into drains, under chrome trim, under emblems, inside wheel wells,
inside bumpers, etc .. blow it off.

i be taking out the carpet before it gets mold and rusts the floor pans,
then work on finding the leaks and drains later.

 

Climb up on a ladder or step stool and look down at the fully opened roof. You'll see the entry openings for the drain tubes at the corners. Do what Stealth has suggested, or use a long, flexible wire or cable and try gently pushing it thru the tube. Then flush it out with water (low or no pressure).

 

wires and cables are fine if you make sure the tip is covered in such a way
that it does not scrape the inner diameter and create more rust spots.

a coat hanger wire probably is not a great choice,
a n insulated single strand 10 gauge wire with the plastic
insulation over the wire tips probably ok. there is also shrink
tubing one can apply as well as "LIQUID ELECTRICAL TAPE",
one of my favorite items in my tool box.

the cars are designed to shed water .. but like the gutters in a house,
the owner has to to a bit of maintenance.

also, let the windows open any time you can to air the car out,
my trunk - Allante - is open when parked in the cave. i place a tennis ball
next to the pull-down to keep the lid from locking down..

bottom line, use good sense ...