It would be pretty difficult to write a guide to address all the different aspects of troubleshooting in this field beyond describing how to isolate a problem when one occurs. Labs also operate differently based on different needs and workloads. I was lucky to have a mentor (Hello Glenn!) and still feel that's the ideal approach to guiding newcomers given the wide range of possible problems and scenarios that can arise. That is more difficult with larger groups. 
Best Wishes.
-Tom Millican

just a research technician