Oh boy. What you have described here is pretty serious.
These systems have been compromised. The fact that you have found a file that details password information awaiting forwarding or retrieval AND a potential delivery method (that is usually what a "bot" does) would suggest that your entire network may be suspect.
I would NOT recommend that you put these systems back into production. The persistent little bot must be coming back from somewhere;, via another program or by repeated breaches. Your best bet for this issue is to restore from backups dating back to BEFORE the breach occurred.
If it was _my_ LAN, or my customer's LAN, I'd be launching a proper investigation, tracing logs and looking for admin accounts and rootkits on all of the servers. I would pull these two servers as a start, back 'em up on brand new media to retain whatever evidence there is left, and then re-install the OS from scratch. Then restore data carefully from older backups.
Next step would be to run a vulnerability scan on everything, and then an organized hardening of all of the systems. Password changes all around, and scan again.
I would also use the backup I created of the compromised system in an isolated lab to glean what Ican about how and when the breach occurred.
You may need the help of a security team or consultant. This is serious stuff.
If you want to stop it from happening again, you need to plan. You need a good policy set, a firewall, an IDS system and maybe even a honeynet. You need to monitor all of these things properly, and consistently.