There is a book called "How to Build and Modify Ford 60 degree V6 engines" by sven pruett. I have a copy of it for my 2.8. It is by no means a real rebuild manual like the chilton v8 rebuilding manual but it does have some valuable information. It is more about a guy spending LOTS of money to get a pretty powerful v-6. I am not sure if it applies to the 4.0 but it is for the 2.6 through 2.9. There might be stuff in there on the 4.0 but im away at school and i dont have it in front of me right now to check. I would recomend this book because its certainly worth the 20 bucks or so that it cost me and its the only book i could find relating specifically to those motors.
Hope this gives you a starting place.

Matt