Excellent plan, breaking it into regions would be the way to go.
SD's limited mass transit system actually corresponds to a pretty scenic brewery tour. There is a Coaster station in Old Town that will get you all the way up to Oceanside, down to downtown San Diego and everywhere in between as well as connect to the Sprinter which will get you into Vista. $12 for an all day pass that is good on both trains.
Here are some spots to check out and their corresponding Coaster / Sprinter stations.
Modern Times: 10 minute walk from the Old Town Coaster Station, very cool setup and excellent beer
Green Flash: 10 minute Uber from the Sorrento Valley Station, huge place with outdoor patio and a huge taplist, also includes Alpine Beers which is a nice bonus. From Green Flash you can get to all of the more inland breweries (Alesmith, Societe, Ballast Point, etc)
Pizza Port and Culture Brewing: 2 minute walk from the Solana Beach station. Pizza port is good spot for their wide selection of beers as well as their excellent pizza. Culture is smaller but worth a shot if you have some time to kill.
The Oceanside stop has bunch of places you can go: Stone, Bagby, Breakwater, 101 Tap House but I wouldn't count those as must-stops. If you're in the area and want a good tap list with good food, look up LTH.
The Sprinter train will get you to downtown Vista which offers Mother Earth, Belching Beaver and Wavelength. A 10 minute Uber from downtown Vista will get you to the Vista business park area which offers Booze Bros, Aztec, Latitude 33, Iron Fist, etc. Out of those I'd recommend Booze Bros, one of the coolest spaces to have a beer as well as a good variety on tap.
Enjoy your trip! You won't be far from good beer no matter where you are in SD.