stephani,
For forward flexion and extension, while standing laterally to the patient, you may place an inclinometer on the shoulder, aligned with the plane of rotation to be measured. The nominal placement of the inclinometer can adjusted to read "zero" and flexion and extension can be measured from that point.
Measurement of lateral flexion can be achieved by placing the inclinometer on the shoulder while facing the patient or centered while at the patients back, depending on the shape of the inclinometer. While these positions may not center at "zero" a bit of simple math may be required for the final angle dimension.
The fact that gravity based inclinometers are always self-calibrated relative to gravity, means that no matter your positioning, you will receive an accurate relative measurement. Of course, your placement must be such that it effectively isolates the joint or joints being measured and should be reasonably aligned with the plane of rotation.
I hope this gives some ideas as to possible measurement
Best wishes,
Doug Montgomery
Independent Design Solutions
We will be offering a new ROM inclinometer for sale in December of 2009.
ROMinclinometer dot com