The Rambam lays down 14 principles, which he terms shorshei mitzvos, to determine which mitzvos are part of the 613. Besides the commentaries in the standard Mishne Torah, are there any other books written on the shorshei mitzvos? Are there shiurim on the shorshei mitzvos available online?
R. Chaim Ilson has a lengthy series of shiurim on this, with several hours per shoresh. These shiurim are available on YUTorah.
From the linked website:
Rav Ilson studied the Shoroshim with Rabbi Joseph B. Soloveitchik zt”l and has been delivering shiurim on the Shoroshim for more than two decades. These shiurim are the basis of the project, a Sefer explicating the Sefer Hamitzvoth.