Hi Andy,
In your photos of post 1432, everywhere you have your red arrows, I used exactly the same black butyl tape on the (Partition Panels, in the EPC), (splash shields, in the US auto industry) that Alfred and Hans used for the plastic door sheets. Note, however, that my car is painted dunkelblau 332 (I call it midnight blue) so the black butyl tape doesn't really show after cleanup with a tiny wooden homemade spatula, although after a few days or weeks, it keeps squeezing out of the joint and has to be re-scraped away. You might prefer to use another type of waterproof sealant (thinner, like caulking, previously mentioned, or tape to make cleanup a one-time job), but if I were you, I would definitely seal the "partition panels" to the inner fender and footwell floor pan in the wheel well.
I suppose you (and everyone else who's done it) have noticed how difficult the outer partition panel seal is to get in the proper position against the inner fender wall. Fun isn't it. I used a homemade metal hook to get behind the rubber lip and pull it out like a cord pulls out the rubber lip of a windshield seal.
Tom Kizer