I have heard of several cases where couples were married after the ninety-day period, but there were usually fines attached by the INS when they applied for adjustment of status.
In each of the above cases, they were married shortly after the ninety day period ? certainly before six months had elapsed.
Technically speaking the Form I-485 Application to Register Permanent Residence or Adjust Status is supposed to be filed with the INS by the ninetieth day that your fianc? is in America.
Consequently, you need to be married about a week or so before that date so that you can get a certified copy of the marriage certificate to include in your application. Don't forget to allow time for the honeymoon if you are planning one out of town.
Depending on your local County Clerk's Office, it may take a few days to a few weeks in order to get your certified copy of the marriage certificate. Ask how long it will take to get your certified copy when you apply for a marriage license.