Unfortunately this is not exactly my particular area of expertise, so for me it's like glimpsing a shadow through smoke and a moving window, mostly an impression but something that has become more and more sophisticated despite my attempts to prevent it via traditional and modern methods of forensics, and even weird things like audible and inaudible platter noise when there shouldn't be heavy (this is the key for me) disk io.
a) How are you identifying the processes? 2) How are you determining that they are inspecting the filesystem?
Process of elimination as far as the processes are concerned. Basically I have been paring back the processes that are visible to me in memory until it should be a bare minimum for a functional Windows kernel in memory, and stubbing out the non-essential processes I find with empty "stubs" so that the hooks are still there but non-functional. Then observing disk io and memory usage, and repeating. Not very scientific, but again, I'm an amateur.
The stuff about disk platter noise is simply recording the audible and inaudible frequencies generated from the platter (I haven't upgraded to a ssd for the system disk yet), and then running regressions on the wave forms to detect anomalies via the noise generated by the platter and the reading head interacting. I was interested in looking into the inaudible frequencies because it seemed like a good way to cloak disk io from the average user.
As far as the botnet stuff, I've done some MITM packet analysis and some simple stuff like tracerts and observing changes in routing. Right now the box is routing all name service through what appears to be another compromised box in the US state of Georgia, though I'm hesitant to do much network topology due to port-scanning being considered the same as cracking.
This is all just a hobby, and I'm sure some of the stuff I've mentioned about is either very crazy sounding or perhaps already known to people more knowledgeable than me. I grew up when pcs were still a weird hobby for society, and so this sort of stuff seems like things we should be able to do without fearing repercussions.
Also, I only posted this to give context to what I had posted before, so take it for whatever you want to. I'm interested in non-violent solutions to improving society and I don't want to jeopardize that.
A lot of this stuff is sort of ephemeral and I don't have any credentials to really convince anyone. That's why I would post this, maybe someone else knows more than me. Like I said, take this as anecdotal and perhaps incorrect... You'll notice a lot of assumptions by me.
If you are genuinely concerned I think it is pretty simple to contact real professionals with whatever data you have.