TL;DR, Why am I getting hit with so much traffic that is not directed towards my actual website? How do I fix it?
I have been diagnosing a problem for ~6 hours now, that I initially thought was a DDOS attack, but it turned out to be related to this:
https://askubuntu.com/questions/802222/random-urls-in-apache-access-log
Now, I have created a default site, and it has blocked nearly everything, but traffic is coming back through and it's chewing into my Linode's limit, as in, 15 GB in that last 12 hours, with no reported users on Google Analytics.
I have searched everywhere for a solution, and have taken measures to prevent DDOS such as module_evasive, but now this traffic is returning and it looks like for some reason my server is receiving requests and getting hit for so much data.
Last chunk of /html/site/logs/access.log when the data and cpu started rising again: https://pastebin.com/wskzGNi9