I was just at SFMW on Fri. and it was empty for the most part.  Multiple rides on Medusa and virtually everything...anyway, to answer your question. 
SFMW does not do anything else outside of the usual Fright Fest haunted houses and spooky themeing.  All rides run normally; nothing is run backwards, in the dark, etc.  So if you were hoping for any changes or re-themeing of the rides for Fright Fest, sorry to disappoint you. 
hope this helps.   
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My current top 5: 
1)Goliath 2)Vertical Velocity(SFMW) 3)Medusa(SFMW) 4)Stealth (PGA) 5)Riddler's Revenge