The CS1064 Spring 2017 project involves modifying a Caesar cipher program to use multiple shift amounts for enhanced encryption. The program will read messages from a file and include transformations such as replacing 'e' with 'zw' and adding 'hokie' around the message before applying character-specific shifts. It allows for both encryption and decryption, with user prompts for file input, shift amounts, and an option to process multiple messages until the user opts to exit.