The re-balance of NPCs was one of the first things I did for Surprise Threat. The only tweaks needed at the time were renaming a few skills, etc. (all of which are detailed on the first page of the doc).
You don't need to use any other house rules, besides what is listed on the document, to use this. And they are all pretty intuitive.
That list of NPCs was used to form and balance other house rules (like Units, Threat Level, Matrix stuff, Amp balancing, etc.) but you don't need to go that far.