Getting the 3D models to look right was quite a struggle and I'm stil not completely there.
I've been klicking a lot in circles with my mouse and I finally gave in by giving KiCad sudo rights to write to /usr/share/kicad/.
Only now the light brighens and I realized I could have temporarily changed the owner of /usr/shar/kicad/
(PS: What's the recommended way to solve this neatly?).
But KiCad did it's thing and I had working Elco's.
Unfortunately this also resulted in a lot of other caps being too small.
This was easily fixed by ditching the whole Capacitor_ThroughHole lib and only using the Capacitor_THT.
Today I thought to just get all the 3D libs from Github (maybe I should just clone) but I did it with KiCad/PcbNew.
After about 10 minutes (It's a 1GB download) the download stopped with the following error:
Error fetching JSON data from URL 'https://raw.githubusercontent.com/KiCad/kicad-library/master/modules/packages3d/Connectors_JST.3dshapes/JST_PH_S10B-PH-K_10x2.00mm_Angled.wrl'.
Reason: 'IO_ERROR: curl_easy_perform()=7: Couldn't connect to server
from /build/kicad-I8aRie/kicad-4.0.6+e0/kicad/common/kicad_curl/kicad_curl_easy.cpp : Perform() : line 92'