After ten months at Hall's Engine in Moreno Valley, I was able to pick it up. To my dissatisfaction, they were not, after all this time, able to get the transmission leak under control, so that's up to me to deal with later. But they did manage to get it to pass smog, the least they could do given that they rebuilt the engine.
In hindsight, I should have done things a bit differently, perhaps finding a different builder or a less expensive one. I get the feeling that after the rebuild was paid for, I was more an annoyance than a customer. So it goes. But we are moving in a few weeks to live at my parents' house in Carlsbad for a month before we can move into the new house in Yorba Linda, and now I got my Jeep back.