How to manually set up the controls on the Nikon D3100 for videography?

I've done everything, but I think the video mode is not affected by the manual controls. The only manual thing that works is the focus. I don't know If the shutter speed setting works fine. One obvious thing that I notice is the ISO. I've pushed down the ISO to ISO 100 and opened the aperture to it's widest point, but still the video looks really grainy

You can't. Other than zoom and focus, you're stuck.

Most DSLRs don't allow much user control in video mode, which was added to sell more cameras, rather than to give serious capability.

The shutter speed is determined by the frame rate you are using, so forget doing that when using your fine digital SLR as a video camera.

Unless you are shooting outdoors or using high output lamps indoors, the ISO will have to automatically increase to assure a good exposure. What that usually means is that the camera will automatically increase the ISO.

It seems that you do not yet understand 1) the fundamentals of photography and 2) the fundamentals of shooting video. An understanding of both is super important if you intend to shoot good video.

Do this

Look at your script and for each scene, layout the lighting you will need, subject position and camera position and framing. This is what is called storyboarding.

I have included two links that should help you with producing your video, but in the end, you are going to have to add a lot of light when shooting indoors.

Some very late dslr cameras allow manual settings during video. Otherwise everything, except as mentioned the focus and zoom, is fully automatic… Nothing you can do.

You expect too much.

The dSLR was never meant to do video so why look for video controls on a video-feature-only camera?