Well, I finally found the leak source this weekend, behind the drivers side kick panel.
The inner seam close to the cowl drain pipe was missing a sealant bead entirely, so much so that you could barely see daylight getting in. My guess is this is normally not a failure point, but given the collision evidence by the dented in cowl side, I think it likely was never repaired correctly in that repair effort. I had to remove one the of fuse panels, disconnect the pull handles, and peel back the NVH padding for the firewall to get to the spot. It's hard to exactly line up where this internal seam is for the outside, but my best guess is the bottom of the drain curve for the (now missing) hose pipe.
I did a duct tape job to test a leak fix for that location and it made a big difference, but didn't stop it entirely, plus leaving tape there would hold moisture to the body. It was nearly impossible to get the caulk gun to the exact spot, but I barely managed to get enough material there to smear into the crack with my finger. I used a silicone RTV sealant this time and we'll see if it passes the leak test after it cures.
The "right" way to do this repair would be a dash out, frame off, re-seam of the entire drivers side cowl area from both the cabin and engine side while also repairing the cowl drain dent. I just can't do that right now so this fix will have to work until then.
For good measure, I patched the popped bottom seam where the cowl meets the door sill with metal HVAC tape.
This repair has been hell and I really want to ring the PO's neck, but at least now the 3-year saga seems to be drawing to a close. To recap what all has been attempted in this repair for future thread finders.
1. New windshield and gasket, double sealed to prevent water leaks (did not fix)
2. 3 attempts to reseal external side cowl drain (did not fix)
3. Cleaned cowl from all debris (did not fix)
4. Metal tape over popped lower seam (did not fix)
5. Tested roof rails and door seals (were not the leak source)
6. Cleaned debris out of lower drivers rear door (unrelated issue, but needed addressing. door was holding water after heavy rain)
The fix: inner cabin seam, estimated to be around the lower drain hose curve fitment.
This could've been done sooner with a more focused approach from myself, but I've learned something new each time I've tried to fix this. Main lesson being,
never underestimate how badly a cheap bastard previous owner will cut corners on a repair. I really think this is the fault of a bum drivers side offset collision repair. I think they slapped a new fender and door on it and called it a day.
If anyone has a a picture of the interior without the dash and wiring harness and/or an external photo sans-fender and drain pipe, I'd love to see it so I can ID the exact location visually.