Updating my 3d models

Just downloaded packages3D-master.zip from Github.

What next?

Unzip it to anywhere you like.
Set KISYS3DMOD to point to the modules/pacages3d (without a final “/”) directory within your unzipped files.
(kicad main window -> preferences -> configure path)

And as a related question, this should solve the mismatched 3d object size issue? I presume I have to re-associate all my placed footprints with the new library, right?

Yes (for now. Until we update more 3d models.)
Assuming you either have the github plugin lib active or you have updated your local footprint lib.

The github plugin might not be the best choice for you. (Something you need to decide.)
If you want a local setup follow the tutorial by @bobc:

You only need to update footprints already placed on the pcb (open the footprint properties of any placed footprint within pcb_new. Open the change footprints dialog and choose exchange all. Or if this does not work reexport the netlist and import it again.)