I just found a strategy so good it's almost cheating.
If you build your vault by skipping every second floor, MoleRats, Rad Roaches, and fires will not be able to spread vertically...
Building your shelter this way you will never have to worry about anything killing off half your vault. You will never have to deal with an infestation in more than one room at a time...
Fires, Roachs and MoleRats will be effectively quarentined to the floor they appear on...
If you need to see the trick in action you can visit my channel on youtube Hail Kira
Where I posted an Overseer's Guide to Fallout Shelter