If you do Stone do the brewery location and get the tour (25 ppl max). The other locations are "just" bars. And if you go to the North County, might as well hit up Lost Abbey and maybe some of the nano-breweries like Indian Joes, Belching Beaver, or Lat33. I assume you're a homebrewer so WhiteLabs would be very educational.
To make a circuit of it:
1) start in the Mira mesa/mar area with Alesmith, Societe, Greenflash, and Hess
2) Cut across to Whitelabs
3) head up the 15 to Stone
4) go west on the 78 to Lost Abbey
5) take San Marcos Blvd (to Palomar apt) and catch Iron Fist/Belching/Lat33/Indian/Aztec/etc
6) back down the 5 to LJ, maybe catch Pizza Port in solana beach but you can skip if you hit lost abbey.