Events-wise, the Great Train Expo will be at the Del Mar Fairgrounds on the weekend of Dec. 7th.
There's also the Pacific Southwest Railway Museum out in Campo that do excursion runs every weekend at 11 and 2pm, but you'll want to plan accordingly as it's about a 60 mile trip out there. If you want to do the Expo plus this one, you're better off to do them on separate days that weekend.
There's the Chula Vista Live Steamers but their earliest run day will be on the following week of your visit.
There's a miniature train ride in Balboa Park right next to the Zoo. Not a long ride, less than 5 minutes, but it's fun enough.
Local hobby stores: San Diego is not known for having any train hobby stores of the caliber of Charles Ro or The Choo Choo barn. Having said that, Frank the Trainman (no website) on Park Blvd several blocks north of the Zoo/Balboa Park, established in 1943, predominantly Lionel with some A/F. Also includes an interesting automobile museum on the left when you go in the store entrance but you have to pay a fee to see that part of it. There's also Reed's Hobbies in La Mesa with a wider variety of trains but still a fairly small shop.
You may also want to check out the historic Santa Fe depot in downtown off of Broadway, and there's also the San Diego Trolley that you can ride around on as well. They also have special Vintage Trolley runs.