Wow, it was really easy once I figured out how to do it.
I all relies on a config.json file. You don't have one? Download the base bootstrap from this link.
The download link is at the very bottom.
Once you have the file, tweak the LESS variables to your heart's content! I put in my brand colors, tweaked a lot of the padding, and some fonts.
Then using the same URL above, upload the config.json and see that all of the variables you changed are reflected in the page. Then simply download it again! Voila!
Note. I tried to add inline comments to the JSON in // and /**/ form, but the parser did not like that at all.