Welcome! The stage 3 Roush has a phase 1 SC kit on it. The phase 1 kit is identifiable in a few ways:
-The TVS SC that sits on top has Roush on it.
-The Phase 1 kit has a closed Roush intake
-The Phase 1 kit comes with an 85mm pulley for the SC
Aftermarket wise the phase 1 kit comes with CARB stickers for under the hood, unsure if these would be a thing from the factory.
As far as verifying the engine I would ask for the bill of sale showing what it was at the time of purchase. If bought private party I would ask if there is an aftermarket tune on it outside of Roush. If bought from a dealer I would consider taking it to a quality tuner to have it tuned properly.