In the scene where the Librarian is climbing down the ladder to the book that has fallen to the floor the title of the book didn't show ver clearly on screen. I lightened it in After FX using the same mask process as I did with the rig removal just with a greatly lightened and edited clean image. I masked the writing on the spine to reveal the lightened writing below.
 
I've finished animating the bookshelf scene! I'm really happy with how it's turned out especially as it is the first scene that I have done. Here are a few photo's of the puppet and set at different stages of the shot:
I realised once I'd moved the puppets hand but onto the ladder after he had dropped the book that I needed him to climb down the ladder. This wasn't something that I had originally planned on doing but I was glad I did as it concluded that shot in a better way. As I hadn't planned on doing this, getting the puupet to look like he was climbing down on the lower rungs was quite difficult due to his size, his closeness to the floor and trying to keep body parts out of shot that had already left. I firstly had to bend his back quite dramatically (<see left image) and then remove the puppet from his hands as his head was getting in the way.

Timelapse of animating the final shot:

 
I spent most of the day setting up the shot for my first scene where the Librarian is up a ladder placing books back onto the shelf.
An initial problem that I came across was the height of the puppet in contrast to the bookshelf in the set up of this shot. The bookshelf needed to take up the whole height and width of the screen but I couldn't achieve this without bending the puppets knees so he would be in the right place for the shot. This caused difficulty because of the ladder and I was having to angle the body which didn't then look right on camera. I found a platform that was essentially a miniature animation table which I could tie down the bookcase whilst raising it slighlty higher so that the puppet would be at the right height without his knees having to be bent (see picture).
Once the shot was set up I wanted to do a few tests with the prototype to warm up my animation skills again. I ended up doing two tests: one shot on ones and the other on twos. I was extremely glad I did this as it has helped me realise what shots I might want to shot on one's (quicker movement e.g. a fast hand swipe) and what I might want to shot on two's (the majority of scenes including this one, it is more controlled and suits the Librarians character better.)

Test One (Shot on ones):

Test Two (Shot on twos):

 
I had built two armatures, both with different sized wire to see which I would prefer animating with; however straight away I realised I didn't even want to try with the smaller sized wire as the puppet was getting a lot of bounce back when even just trying to position him on screen. These tests are all therefore with the one armature.

I thought I would try animating the scene where he's at the bookcase throwing books to the floor and also the scene where he walks across the screen dragging the book along behind him. My animating skills are currently VERY rusty so I am now getting back into the swing of things.

Bookshelf test 1:

I almost cried when I first watched this back. It became obvious to me that I was trying to add in lots of unnecessary movements which were complicating the point of the movements he was actually trying to make. Also the speed of the book falling was way too slow.

Bookshelf test 2:

I felt like the animation worked a lot better with simpler movements, I also tried leaving more frames in between movements so as not to feel rushed.

Bookshelf test 3:

This test was the most controlled so far. The one problem I did find was that not having a physical bookshelf to reach out to and pluck a book from meant that I was unsure where his hand should exactly be at that point to the action seems slightly confused. I will do another test with props in the the near future.

Walk test:

I have never animated a puppet with tie downs before, only pins so this was a completely new experience. I felt like he was shuffling more than walking but in a way this adds to his characteristic of being an old, miserable man. I'm going to try this again but swap the hands over so that the hand holding the book is on the side of the camera, I think the swinging arm might not be so in the way if it were further from the camera.