Does special indictments count towards the mandatory 3 terms ?
Indictments have nothing to do with sentencing issues or guidelines. They are a formal naming of a person to a particular crime. It's common for charges to result in an indictment that long after arrest. You're innocent until proven guilty in a court of law, so no, an indictment by itself doesn't mean automatic jail time.
To obtain an indictment against a suspected criminal, the prosecutor must present their case to a grand jury. A grand jury is a jury made of a group of 16-40 local citizens who are sworn in as a jury about every 18 months. A grand jury differs from a trial jury, as the grand jury is required to sit for a much longer period of time than a trial jury is required.
There is no judge involved in a grand jury proceeding, and unlike a trial jury, which hears equally from all parties in a criminal case, the grand jury is considered to be an arm of the prosecution, and generally hears only from the prosecution. The old adage relating to this is "a prosecutor can indict a ham sandwich". For this one-sided arrangement, indictments are fairly easy for the prosecution to obtain.