How to do multiple exposure effect with Nikon D90?

I have been wanting to do some shots similar to these shots, found in this tutorial:
http://vsco.co/features/sara-k-byrne-tutorial-vsco-film

There's a video tutorial that she explains how to, but my camera doesn't have the same things to make it that easy on me. Any help would be great!

The D90 does have a multiple exposure mode, but I don't think it has the same depth of creative control in-camera that the Canon 5D Mark III has.

To do multiple exposure on a D90:

select multiple exposure from the Shooting Menu, then select the options; number of shots, auto gain, etc. Gain will make sure that the resultant photo is exposed correctly, and should be left in Auto unless it is not working for a particular shot.

Then select DONE and take the photos.

The camera will revert to normal mode when you have taken the number of photos you selected.

I have done this on my D90, so I can confirm it works.

Why does the first photo not align properly with the other two