Thanks for posting this, especially the note that your own server was already attacked.
If exploitation actually reached the server, I wouldn't stop at upgrading CSF or setting MESSENGERV3 = 0. Those close the known entry point, but they don't establish whether anything was left behind.
I would also check recent systemd service creation/modification, unexpected cron entries, new or modified SSH authorized_keys, unusual listening ports/processes, recent executables in /tmp and similar writable locations, and suspicious processes that return after being killed.
Comparing timestamps around the suspected attack window can be particularly useful. If something was executed as the Apache user, I'd also inspect files/directories writable by that context and correlate them with the web/access logs.
I develop the CWP7 Security Audit Module, which automates a number of these evidence checks specifically for CWP7 servers and reports them as PASS / INFO / REVIEW / FAIL. I built it largely because checking these persistence indicators manually after CWP incidents became repetitive. If useful, I can explain the checks it performs — but regardless of the tool, I would definitely do a post-compromise review after applying the CSF fix.