I am running a store championship at the tail end of the circuit and my question is are the scum and villainy ships now tournament legal in the store championships because they are not legal in the new tournament faq?

Yup they are. New Tournament Rules as of today.

https://images-cdn.fantasyflightgames.com/filer_public/d6/2c/d62c343a-c4bd-497f-a45c-7cf0dd2cb300/x-wing_tournamentrules_v223.pdf