Hi,

Currently stuck at Dead Nations, I am supposed to kill six rats in the western part of the area but they are nowhere to be found. I haven't killed Soego or anything yet. I think the game is bugging out somehow.

The quests I am supposed to be receiving here don't even show up in my journal.
What gives?

Yup, still bugged. I am at the caved in corridor and still no rats. I've looked up videos where other people have them but I see no rats at all. I tried starting back from Pharod with another save but still no rats.

Is re-installing some of the mods recommended? Or do I just have to kill everyone?

Could be a bug then. Have you installed the recommended mods? They do fix many bugs. Also, it's better not to install the widescreen mod, it just creates too many issues and also the game tends to crash a lot with that mod installed. As an additional step to try, you can also reload from an earlier save if you have one, and see if you still encounter that problem.