Earlier quoted context omitted.
Until you restore from backup: then you probably have a compromised system again.
If you restore data from backup you're fine. Configuration should be re-applied. Unfortunately you need to check every file with an executable bit that comes out of your backups - review shell scripts, recompile executables. It's rare that attackers tamper with data, usually they just leak it. Source code may be targeted though.
buffer overflows in non-executable files means it's easy for someone who wants to, to recompromise a machine: pdf, gif, jpg, whatever.