If anyone is having a problem with the two file thing, where you get the doomsday and mini-scenarios instead of the MDS, here is a easy fix. There might be some problems with this, that I'm not sure of because I am getting some random pauses and stuff, but usually it works.
Simply remove all the content from each of the two downloaded files and place the content directly into the file you created in the Mods file. From there the game should launch and perform, though again, I am uncertain if you will receive the same strange glitches I have.