If you had Nuetral Reputation with NCR or Vaulty City when you joined Raiders, then got SM 3 and immidiatly left, then the worse you could be is Hated with Vault Cty and NCR, which means that you are not shot on sight in the towns.You can kill "Slavers" (found near Den) to increase your reputation with NCR, not sure about Vault City.
If you resigned from the Raiders, the only thing that affects you is ReputationIf you are anything below Neutral (Antipathy or Hated) then you will be attacked by that faction in Random Encounters.(e.g. Antipathy with NCR = NCR Caravan attacks you on sight)But since you are not Vilified with NCR or any other faction, you will not be shot on sight in cities, and you can usually escape any encounters with NCR caravan, rangers, etc, until your Reputation goes uo, or you kill some slavers to bring your rep up (only confirmed that it brings NCR reputation up)