The passenger side is bone dry (but I am pulling that side apart to also POR-15 and cavity wax for good measure). I am also going to spray inside the frame rails while there - there are plastic access covers under the tar. I pulled the carpets and scraped off the factory tar mats last night and the floor pans are solid but were wet (ouch). So given that water can get in the rockers (and subsequently into the floors) several ways as you say - from the front, rear windows, etc, my question is how is it supposed to drain? When I get the car on jack stands I will compare sides to see why one drained and the other did not.
I did not mean to say that the incoming source of H20 was definitely the front wheel well - floor area. Since this was the source of my unwanted humidity, I thought I would suggest a starting place for your search. (Livingston and Stanley began their respective searches in Africa.) In my experience, regardless of condition, few E9s are absolutely water-tight up top near the side windows, and even fewer E9 owners would readily submit their cars for clinical hose down trials with fire department pumpers. Commander Murray would certainly understand.
You raise an interesting point about "natural" or intended drain holes. I once spent a lonely weekend with a wet vac on both an 02 (type 114/E10) and and E3 that were inadvertently left outside with windows partially open during a torrential cloud burst. (IIRC, they were outside due to the driveway having been freshly repaved.) Both cars retained about an inch of water in various areas - without any obvious dripping. I toyed with the idea of drilling some drain holes, but resisted in favor of the wet vac., dessicants and assorted unapproved dehumidification methodology. Everything turned out fine with the added benefit that the interiors received a much needed cleaning and I discovered some loose change. It turns out that both vehicles had been treated with Ziebart Rust treatment/undercoating, and that probably plugged any obvious drain holes. (The '02 has a box-like enclosure for brake and clutch master assemblies. As best I can recall, it did not have any drainage holes, which is probably why it is often a source of iron oxide.)
I am unaware of any E9 body pan drain holes, although I seem to recall at least one or two examples of dangling rubber tubes, that may have been a means of venting batteries stored under the rear seats. Sadly, I would image that many E9s and other cars of their ilk and age have developed their own moisture disposal systems and it is a positive testament that yours is solid. That said, I would seriously consider tapping a couple of holes in non-strategic low areas, with the notion that they could easily be plugged with something like 3M 5200, commonly used to seal boat transom seams or some other seam sealant. Rubber plugs typically generally don't cut it. I think this is better than the alternative of waiting for evaporation or shipping the car to the Sahara, in search of Lawrence. I am also reminded of the example set by Dang, where he parks in car on a downward sloping driveway as a deterrent to unwanted water collection.
It might be that similarly jacking your car fore or aft will reveal some hidden weep holes.
Wish I had a better response, other than to say what you already know, get rid of that water ASAP or consider adopting pet sea sponges.
Best of luck.