So, I put the cubes edge-to-edge so when I remove doubles, it will be one cube (with a loop cut in the middle). When I join them and remove double vertices, it removes one face, but not the other face.
Is there any way to remove that face without doing it manually? I am modeling this type of stuff on a HUGE scale, and I don’t have time to remove the faces.
Remove doubles removes vertices.
After doing that you could try selecting them with select menu -> interior faces and then delete those faces with X -> faces.
What you have in the pic doesn’t count as an interior face but it’s non-manifold (which you could also select) but you also have other non-manifold elements in that pic. Combination of the two should allow you to find and get rid of bad geometry.