My water in the footwell issues seems to be windscreen seal related. When I knew there was a good chance of rain I gaffa taped all around the windscreen seal as a test. Not a drop of water found on the floor. Pulled the tape off and hey presto - water again. (Don't leave tape on too long and take care removing it. I left mine on about 2-3 days and it came off without issues)
The dealer sealed it up with a bead of sealant under the windscreen rubber. Had a reasonable amount of rain since and it seems to be holding up so far.
The Water Ingress Manual seems to have been superseded by "Water Leak Diagnostic Procedure" in the Workshop Manual. The dealer provided me with a Tech Bulletin which then referred to section 501-25C in the workshop manual.

