Sorry to hear of the problems with your car. I think you'll find people here quite helpful in spite of the few replies received on this thread so far.
Leaking vapor barriers in the doors result in water in the footwells, i.e. soggy carpets. Based on the posts here and b-forums, rear door leaks are common, front doors rare. The door configuration is such that if the barrier sealant separates from the door structure, water does drip just inside the sill and down into the footwell. There are repair DIYs.
EDIT: soggy carpet will be found at the footwell for the door leaking.
Water in the headliner is most likely from the sunroof. The "cassette" is the sunroof assembly including frame, drip pan, tracks, motor, seals etc. It's termed a cassette because it can be removed & installed as a single unit. But removal is not required for most repairs. There are drains front and rear, each side. Reported leaks are not particularly common problem, but a real PITA when they happen. There are repair DIYs.
For E39 diagnosis guides & repairs have a look at the first two posts ("stickies") on page one of this forum.
1) How to easily find information ...
2) the VERY best of of E39 links
You will find a comprehensive list of references, guides & DIYs.
The third sticky is usefull too.
If you don't find help after a seach, post back with specifics of what you need help with.
Last edited by rdl; 03-01-2013 at 04:12 PM.