Thank you so much tigran! I was going around in circles with this last night for hours!
I will make sure to download the correct package in future use of github.com
I started from scratched, using Kite this time and with the correct files, it worked straight away.
With the nightly build, the files were already separated in to the correct directories and so just dropped them straight on to Kindle, instead of following installation guide which suggested putting them in 'customupdates' first. This leaves me wondering what's the deal with that directory? Does it make any difference that I didn't use it?