Since 2-4 are submitted electronically, the problem probably isn't there, otherwise you wouldn't have been able to submit your application. I think that for Stony Brook you need to mail transcripts in an official folder from your institution (or let your institution mail them for you). Are you sure you did this procedure right? Anyway, I suggest that you send an e-mail to the department's secretary who's responsible for the graduate program, in order to find out what is missing.
I, myself, have not applied to Stony Brook, but I know from friends that they have sent them an e-mail sometime ago saying that they have recieved all their application material.