I live in San Diego, be happy to chat with you offline and help you make the most of your time while you're in town. email me at the address in my profile and we can connect.
as you said the SD Model Railroad Museum is a must. And since its in Balboa Park there are tens of San Diego's best museum all there (Automobile History Museum, Air & Space Museum, Sports Hall of Fame Museum, Natural History, Photography Museum, San Diego Historical Society, and on and on)
a five minute walk from the Model Railroad Museum is San Diego Zoo. And they operate the most wonderful outdoor train. Modeled in Daylight livery with a Diesel F3 and approximately 10 passenger cars that each sit one adult. Its about a 10 minute ride. Sometimes my boys don't want to ride it when we go to the zoo but I still buy tickets and ride it 2-3 times. A blast.
As someone else mentioned theres a new wonderful layout in Old Town, privately owned, free admission and a sight to behold. Must see. http://www.oldtownmodelrailroaddepot.com
There's also the historic National City (south of downtown) Historic Train Depot and home to the San Diego Electric Railway Association. 2 o gauge operating layouts and lots of train history.
and you must make time to ride the most beautiful fully restored electric trolley downtown. Go the web site I couldn't possibly do it justice. I often see it running on my way to work downtown and it never gets old. you should definitely make time to ride it, circles downtown great way to see the city. http://www.sdvintagetrolley.com
Depending when you are here I'd be happy to give you a whirlwind tour of all of the above. We love showing off our town.
And there's no strangers in our hobby.