The swapfile was set to 2-4GB, and when viewing system files I never saw it anything but 2GB.

It looks like the problem was with one of our sql databases. A 50MB test database was creating a 178GB log file on the D: drive of the system. Setting the recovery model to "Simple" and making sure "Auto Shrink" was turned on fixed it(along with a manual shrink). Took the log file down to 23MB. So it looks like it was using the system drive while creating/updating that outrageous log file. Definitely something messed up there. Fortunately it was related to just the one database, which will be deleted this week as we get ready to load actual data to go live with.

Thanks again everyone!