This is kinda tricky, but it works:
- Draw a rectangle the same size as and positioned directly atop your video.
- Select your custom shape and bring it to front, then move it atop the rectangle and video so it sits over the part of the video you want to crop to.
- Select the rectangle and custom shape then in the shape format tab, insert group, choose Merge Shapes and choose to Subtract. This will create a hole in the rectangle the same size as your custom shape (Undo then select the two in the opposite order and try again if it doesn't work.)
- Now select this new shape with a hole in it and set its fill to Slide Background, and give it no outline.
- Try playing the show now.