Ok, to assist in the calibration and resetting the chains, I will point you to this page: WebControl: how to use the basic and advanced features
That is a super simple page to follow, as well as includes some videos that @Orob put together (I think he did the whole page as well) to show the exact steps. That would be where I would (and have) start.
As for that capacitor, in my very limited knowledge, it’s position right by that barrel connection to the board would tell me that it would regulate the power to the Arduino coming in through that connection. As it shouldn’t be used because the power would come from the USB connection, that is where I was saying “it shouldn’t matter” but I could very well be wrong. If you move that barrel connection from the power supply up to the shield as it should be, then that capacitor shouldn’t have any play when it comes to the 12v power.
I was thinking you could test that and plug the usb into the arduino, and the power into the shield and see if you still get board recognition, and can then move the motors as they now have the requisite power needed.