Right now im using a simple event based random...
Variable set up as 'Random'
event
Control Variable - Random - random between 0-whatever your chances...
conditional if Random is 1 or whatever...
weather blah
screentintblah
anything else blah... (if you want lighting make another variable as Storm and set it up as i describe below)
conditional if Random is Blah or Blah
weather none
screen tint 0 0 0 blah
anything else to normal...
then wait blah to your chances...
storm event
control variable random 0 to whatever
if random is blah
screen flash -blah
(wait or immediate sound)-blah blah...
wait to whatever you want...
sorry about the blahs... i don't feel like i should have to do examples for something simple...

this works in a way... just do different things for certain areas...