So I finally found WHICH variable to alter.
My "temp" settings within Media Encoder AND AE (Cache Folders, etc) were all set to the correct drives. However, there was ONE cache within After Effects itself that was set to use the C:\Temp folder.
Sorry Mylenium, Adobe needs to design a better menu system where within the program I'm using, I can adjust said variable without having to be smart enough to deduce that the Adobe Media Encoder is using the After Effects engine within Task Manager and thus, the cache setting you really want to change is within After Effects, NOT Media Encoder.
If we know that PP, AE, and AME all handshake with each other, you'd think each program would have the same, universally linked cache settings, while still allowing Project settings to be separate within PP or AE like we currently have, but that you can change the SAME cache settings for ALL programs OR set independent cache's per program (if I decide to get three Barracuda 10k RPM drives to make exclusive for cache, and set one for each program when doing live previews so I can stop wearing out SSD's). That if I originally start a project in PP, find out I need AE, move to AE after setting all of my cache's within AME/PP the way I want, spend years not knowing I'm trashing my C: drive because of the shader within that program being set to something else. Adobe needs to have ALL shader cache's and folder definitions on ONE page where someone can set control across ALL programs because many of us learn this stuff as we go, and we don't need variables strewn across the programs that you need to hunt down and "know" to be another limiting factor for us.
As I said before, my original confusion is because you cannot adjust this specific cache setting within Adobe Media Encoder; you have to load After Effects and change it there. What may seem obvious to you, may be from being taught this information, but a bad menu design is a bad menu design.