You do not want to file your individual return prior to the 1120S being accepted. It will further confuse their whole process.
I will assume that the IRS will have processed your return by the 16th or 17th of March, as they will be proactive in seeing who is a day late in filing. Contact them again by the 17th and see if they have a record of receiving it. Wait until they have it before filing your 1040. Obviously do not wait beyond the April 18th deadline.
