I have a v2 for mine. And no you do not have to have an intake for stage 2. But they do support one if its in the map notes(convey Sf intake). Paul is right though, I would call Cobb and verify if they give you a credit towards a v2 if you send them the old one. It's well worth it for that price imo. As for you last statement, I think you are mistaking the ap-sub-001 for what you are thinking the v2 is. All the sub-001 is, is the model number of the ap.Cobb doesn't even list the v1 anywhere on their website anymore. But at the top of the website is a direct phone number for them and I understand they have great customer service.
Cobb ap stage 2 ots, catless uppipe, catless turboback, Cobb Sf intake.