A few formatting changes mostly on the tables of content/figures.

Hi Lane,

Would you please take a look at these changes at your convenience and merge them to the master repository? 
I can not completely recall but the major revision I've made were basically on tables of contents/figures, acknowledge page and appendices. The package should generate the sample pages which are exactly the same as which in the word version. Hope they will be helpful to you and future PhD graduates.

Best,

Yi