lazy-e, I’m like you, a total novice in all this Putty stuff but since I succeeded in finally resolving this whole mess, let me see if I can offer a little help.
So I’m not going to tell you how to remove Plex but how I got the whole thing to work.
I’m going to assume you are as ignorant as I was.
Putty…I’ve found it to be very erratic. Sometimes it would work, other times not and yet I seemed to be doing the exact same thing. So there already, my advice is try the same thing many times with minor variations like restarting Putty or the Plex server (I even restarted the NAS!).
The pasting of the password in Putty is done by Shift+Insert key. Important…you will not see the password! It appears as if you had done nothing but it’s there, just press Enter after that.
This is the part that was most erratic for me and caused me to restart Putty many times because it often resulted in an error and refusing me access
Then - I don’t know if you fell victim to Deadbolt? - I realized I had changed the default port for SSH on the NAS which was normally Port 22 as is default in Putty. So matching the two ports finally got me in the NAS through Putty (had changed it because the Deabolt attack).
For now, I won’t go any further as getting this far is a prerequisite for any problems that might come after. But rest assured, after that it gets easier as is just a matter of getting familiar with a few Linux commands which I will gladly help you with if necessary.
PS I also had forgotten to stop Plex as given in these instructions. In fact, you are better off looking for help on that thread which is more specifically geared towards the tool as it applies to Linux-based NAS like the QNAP.
I hope some of this will help…hang in there! 
