As it's written this seems to be a very confused article to me. What exactly is the author's point in writing this? And what is his next step moving forward?
What operating system does he use, what software under that operating system (specifically the FTP client), does he have a secure firewall, etc. etc.
Can you tell me what your next steps in proceeding are, or would this violate the protection you're attempting to set up?
Helpful advice is more than welcome.
But you should try to script something quickly which will automate these actions for you. And you should also try to make a bot to investigate the "backdoor" more.
Aside from your evidence, is there anything that has happened in the past that would lead you to being a target for the NCIS?
1. If you suspect the machine was tampered with, do not use it again. There are a lot of places a backdoor could be hiding, even after you reinstall the OS.
2. If you do not do so already, use smartcards for crypto. Don't store keys on your machine. It is easier to carry a card around than a computer, and smartcards are harder to brute force.
If you're doing really security sensitive work don't run questionable software which you don't have the source code for.