You can set the camera to ignore the achieved focus status.
An SB-600/700/800/900/910 or SU-800 used IR to create focus marks and many times can achieve focus when the white focus assist light can not.
If the camera can not auto focus, then you will have to manually focus the camera. There should be a M/A switch on the camera body and lens.
With more understanding of DOF, Depth of Field, you could set your camera to f8 and then select the DOF distance to include the area you are interested in. You should be able to get an image with an acceptable range of focused image.