Hey Ryan,
If you wanna check out the Zoo, recommend the San Diego Safari Park over the San Diego Zoo (same group, two different locations). The Safari park is about 30 minutes north of the city in Escondido (where I live actually) and sort of nicer to walk around and enjoy. Less touristy too. The on in town is nice too, and is literally in Balboa Park (with tons of museums to see on it's own), but we prefer the Safari Park (have annual passes).
As for nice Drives in the Mustang. You could run this loop. 150 miles and takes you from San Diego, out the 8 East, off into Pine Valley and up the Sunrise Hwy, across the mountain ridge with great views way down into the desert floor, off to Julian the old mining town, great to walk around and eat, down from the mountains to Santa Ysabel, apple pie at the Santa Ysabel 79/78 junction, down 78 past the Safari Park, into Escondido (wave as you drive by) for a drink at Stone, then onto Del Dios Hwy through the very high $$ neighborhoods, down into Solana Beach, then take the PCH Hwy 1 down through Del Mar and into La Jolla and back to SD.
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Let me know what else you are interested in and I can give you some reco's.