I'm sure there is more science to this than I am familiar with, but I think there are some fairly simple considerations that might help.
1)The walls with the clerestory windows should be far enough apart that the light coming into the window does not just hit the wall on the other side w/o getting into the shop.
2) The usefulness of the clerestories will be very dependent on the orientation of the building relative to the path of the sun. If one side of the clerestory faces south, that's probably as good as it can get as far as maximizing the amount of light that can come in on a given day. Consequently, I'm not sure there's much benefit in windows and their associated vertical wall on the side that faces away from the sun. It will never face the sun unless the building moves. If you look at clerestories on old factories, they use a sloped roof rising to the top of the clerestories from the "north" wall and then the roof on the south side meets the bottom of the clerestories. Usually, the windows comprise all or most of the vertical surface between the roof sections. There are several ways that this can be accomplished
3) Obviously, the angle of the sun is going to make a big difference in how much light you get. Not sure where you live, but if you're in the north then the sun never gets very high in the winter sky. I think someone in the solar panel business could probably help you figure out the seasonal inclination of the sun in your area and from that you could figure out the geometry of the building to get the most benefit. Maximize the solar gain(Light=HEAT) in the winter when it's cold and dark and less optimal in the summer when it's hot or whatever you feel would be best for you.
Just some quick thoughts. I'm not a clerestory engineer. Hope it works out well.