I needed to remove a fishing wire rig from the tree in the wind shot, however the clean image process wasn't going to work with this one as I would have needed a clean image for each frame due to the moving shadow across the floor. After some experimentation I realised I could paint out the rig in After FX, using the colour eyedropper tool to select the colour nearest to each section of the rig in paint a few pixels at a time.

Example of a section of the wire that has been painted:

The whole wire has been painted out:

This was a long and tedious process as I had to do it hundreds of times on each individual frame, but the outcome worked well in the moving image.

In the bookshelf scene I needed to remove a rig that appears in a few frames of the shot which supports the books that falls to the floor.
I imported the footage into After FX with a 'clean image' behind it(a JPEG image that doesn't contain the rig, the background with nothing in front of it).

I used the pen tool to create a mask around the rig and then ticked the inverted box on the mask layer. This bought the clean image inside the masked area removing the rig.

I then made sure to move the mask out of the way on the other frames so they were not affected too.

I noticed that an unwanted shadow also appears in this shot near the end. I applied the same masking process to the shadow and was able to remove this aswell.

I also had to animate the z's in a second shot, however this was much easier as they didn't have to interact with the puppet.

To get them to blow off of the tree I simply added two position points in After FX and curved the motion line. I then added a high rotation through this path of movement.

I am now half way through animating my last group of shots: the book. I firstly shot the writing and page turn shot.
Here is a test for the writing:

I then needed to shoot the tree blowing followed by it 'growing'. Here is a test for both of these shots:

I used fishing wire to create the tree blowing which I will need to remove in After FX. The hands in this test show how the tree should grow, at what speeds during different stages and twisting whilst growing.

I shot the tree growing last as I need to destroy it to be able to do so, which meant that I had to get it in one shot. This would be filmed in reverse so the tree would originally look like it is destroying itself, but I will then reverse the images so it plays as if the tree is growing.

The tree scene before reversed: