Ok, so I pulled Smaug and immediately noticed the problem. There is a small metal tab that fits between the optical switches and mine was bent enough so it wouldn't fit. I used needle nose pliers to gently bend it back. Even after some careful adjustments the tab was still too long, so I took a dremel and ground off a small amount of the tab.
After that I noticed that the chip that is socketed on the board underneath Smaug was damaged as well. One of the screws that holds the servo/jaw bracket in place sticks out the bottom near the chip. When I was testing to see if the metal tab would fit between the optos I turned Smaug too far and damaged the chip and the socket by hitting the screw. Anyway, put it all back together and still doesn't register end points. Probably damaged the chip or the socket.
I don't think my Smaug ever worked straight from the factory. The metal tab is so strong that there is no way the motor on Smaug could have bent it.