Hi,
Unfortunately there is not yet an updated user guide, however, most changes between 3.9 and 4.2 have been modest - at least on the chem side of things. You can see a list of documented changes here:
https://github.com/wrf-model/WRF/releases
and chem-specific pull requests here:
https://github.com/wrf-model/WRF/pulls?q=is%3Apr+label%3A%22WRF+Chem%22+
We will be working on putting out a new user guide soon - Is there something specific you would like to see discussed?
Jordan