I agree with Anne that the gyros, even at Shish or Black Sea, are not really like the ubiquitous German doner--the bread, the meat, and the sauce are all very different. Both restaurants do serve nice gyro sandwiches, though, and are worth visiting on their own merits.
A better substitute might be a lamb or beef kebab sandwich. You will get the pleasing chewiness of the meat (missing in the pressed gyro) with a similar flavor profile (lemon, oregano, garlic).
The beans are actually very different. In the TJ's along I-169, the beans are heavily seasoned while in Sioux Falls, they're very plain and require buckets of hot sauce.
As for other SF picks--Lalibela is very good. Cafe 334 is good. Spezia can be really good or really terrible. Dishes there are rarely the same twice.
Generally, if you scale down expectations--especially of wine lists and quality of non-meat ingredients--the food is generally ok, sometimes even good (Keg chicken, for instance), though not usually very good for you.