When I lived on the peninsula in college I would often do a night run along the peninsula, up Superior (big hill), then cut right at the first intersection at the top and go past Hoag. You can cross Newport Blvd and then run along Cliff drive, up above PCH. It is a nice area and well lit. Then I would either loop around back the same way, or head down Dover and return on PCH. Obviously, depending on where you start, you can do parts of this or the whole loop. I am a female and generally very cautious, but this loop has always felt safe and decently populated with people or cars.
I avoid the more secluded side of Back Bay at night. I will run on the side that runs along Irvine Ave, and you can extend that run at the southern end by jumping onto Santiago Dr, which eventually takes you up to Castaways. You can return the same way, or run back up Dover to hit Irvine.
Also, around UC Irvine would be pretty safe and well lit. There is an outer circle on the road, an inner circle through the buildings on campus, and then a third circle around the park in the middle of campus. That could keep you entertained.