I think the hacker got access in my computer, while I was performing a backup on my external drive, and for the time the (possible) rootkit gave him access to my computer (in real time), he made a copy of a lot of information that were accessible from my external drive - one of them being a text document with all my keys that usually stays on that external drive. With that in their hands, the rest is quite easy to figure out.
But how and where I got a malware in my computer, this I'm truely unsure.