I reckon you, me, a torch, a garden hose and about 10 minutes ought to find it.
It could be coming in through the side windows, particularly if the door seals are penetrated by roof bar mounting clips (you don't have a garage so we can't see). Your winding-window seals could be letting water into the door and if the inner membrane has been damaged/removed, water could be making its way onto the door panel (where your speaker mounts to) and into the cabin.
The windscreen is a definite possibility, but check for ingress through the venting at the front first. I'm just wondering if it's entering your air conditioning passageways and dropping on the floor that way. Then I'd spray around the windscreen - pay particular attention to the area along the top, I recall something about windscreen sealing problems in that area.
D40s had an issue where some of the cars had shorter drainage hoses that popped out of the firewall and leaked condensate into the cabin, but that happens on hot humid days, not just when it rains. I'd still check that too, just in case.