The second edition of the O'Reilly handbook Software Portability with imake was written while the current X Window System release was X11R6.1. X11R6.3 was released December 23, 1996. However, R6.1 and R6.3 are highly compatible. As far as I am currently aware, almost everything in the handbook that is intended to apply to R6.1 can be applied without change to R6.3. I'll be posting a list of gotcha's to watch out for shortly. In the meantime, I've written up some observations on the R6.3 configuration files and programs; they're available in the imake-stuff archives.
The itools software distribution was originally based on R6.1. A distribution based on R6.3 is now available.