Sharky's now has a gluten free menu. If you ask in the restaurant, there is a one page menu to order from. It only appeared effective December 2012, so is very recent. I have not located a copy on the website, but if you find it online please add the link as a comment. They must have had a GF menu training recently...The cook was aware of cross contamination issues, he even mentioned that although the chips are made from corn, they are cross contaminated in the fryer....so are not gluten free. The corn tortillas are prepared on a different griddle than the flour to prevent CC. There is even an AJ burrito bowl on the GF menu that is not on the regular menu. I was at the Simi Valley location...if you'd like to go to the place that seemed on top of things. The other locations are also supposed to offer and be aware of the GF menu items.
Here is the link to Sharky's Gluten Free Options
It is a PDF file.