If it's any help, I've got an occasional leak into the rear passenger footwell of my 156 SW. It comes from the rear door speaker. Water comes through the window seal, down the inside of the door and then gets caught up on the inside if the door liner. There's a hole in this for the speaker cable, through which the water gets in. It then gets past the door seal by dripping out if the corner of the door card. Bloody annoying, as I've not been able to seal it yet.
If yours is a three door it might not be this though...
Edited to add... Read the OP again... It's a three door d'oh.
If the door go past the front seats though it could still be worth a look.