This shop is also in Miramar:
http://www.sdtruckshop.com/
I have used both of those shops. The owner of San Diego Truck Shop is the son of the owner of Protrux in San Marcos.
For a newer model vehicle I'd go to San Diego Truck Shop. For older Cruisers I'd go to SDTRUX. My opinion...
I've also mentioned The Truck Shop (sdtruckshop.com) in this post I think. I just had some work done there before Christmas, and James is very honest whenever I take my Cruiser to him.
I've seen some of their custom tube work and it is very nice. I might have him build me a front bumper...
I know this is a little late but PROTRUX in San Marcos (North County) has a good reputation for reliable work on Toyota trucks. I know several people who service their trucks here:
http://www.protrux.net/
Closer to San Diego proper I take my LC to The Truck Shop. I have been very pleased...