Haha good old Phil McCavity
Any of that stuff is great. For the erm, 'cavities' I filled mine with Wurth wax, which as mentioned, comes with a nice long shaft for filling cavities
All the chassis leg box sections, all the factory mounting jig bungs etc etc, get fill all those dark holes with your long shaft
The main issue with old MK5s is the rot hiding behind the plastic sill covers, and the factory e-coat breaks down over the years which looks OK visually, especially behind the perma-damp arch liners, but you may find heap big rust spots when it's sanded back. My 2007 ED30 was pretty much a restoration project when I saw all that, which I couldn't be bothered with, so moved it on