Most of the documentation needed for this project was found on Atmel's website, http://www.atmel.com. While working on this project (2002 Q1, Q2), it was available in PDF format, free for downloading.
The specific documents that were used are:
"AVR Instruction Set", Atmel Corporation
Datasheets for the controllers:
While designing pAVR's pipeline, I found many interesting ideas in the book "Computer architecture - a quantitative approach", by J. Hennessy and D. Patterson. If you are a processor designer, then this book is for you.