Often when the components are of incorrect size, the scaling issue is due to SI vs imperial units. That is, that the 1.0000 scaling should be divided by 2.54 (one inch is 2.54 cm): 1.0000 --> 0.3937007874...
However, this is against KiCad library convention, stating that good practice is using scaling 1.00 in all directions.
The by far easiest fix is to install FreeCad and add a macro
which is designed to make life easier when working with footprints and 3D-components in KiCad. The macro is called "KiCad StepUp", and adds a bunch of tools to FreeCad, including automatic rescaling and so forth. It also makes much better renders (photo realistic).
Grab it here: https://sourceforge.net/projects/kicadstepup/
Image showing FreeCad with the StepUp tools to the right of the capacitor. You can import mod-files, pcb-files, etc and export to STEP and WRML (with automatic rescaling and color selection to different parts).
It is also easy to move components to make them fit the footprints. This is a pain in the ass in KiCad.
(This post was originally much longer with more pictures and relevant links, but because I am a new user here, I was not allowed to post it as there is a limit of 1 pic and 2 links......)