Hello Compsos,
What I have found in many cases is that the script which is allowing the injection is way way from where these malicious files are located, as if the hacker / bot uploaded the script into the same directory of the script they are using to inject then it would be easy to find and fix. So they tend to upload tens of files maliciously and then come back to them a few months later to play havoc as you likely won't have a backup old enough to restore and update.
The key is to be kept up to date. I would advise using the likes of watchful.li, doing a full malware scan. This checks the original checksums of the Joomla! files.
You should then look at the likes of Akeeba Admin tools to improve your .htaccess security, whilst using the WAF (firewall). Once that is done, you can then setup the filewatcher. If any files are modified since the lastscan it will notify you of the file that has been modified.
Many thanks
Tony
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