I think if you go to a podcast player (like iTunes) and search Len Testa you can find some podcasts where Len explains some of your questions. @len, are there any articles that answer some of these questions?
The book came first, as is usually the case. The Unofficial Guide to Walt Disney World by Bob Sehlinger and Len Testa was the starting point for Touring Plans.
From what I have read, Len started all this with doing his PhD. He would walk around Magic Kingdom and record the times listed and had friends that would record the times they were in line and he matched those up. The computer program did come before the book. Here is a link about all this and how it started.