I am an architect working on some historic structures. What engineering protocols and assumptions do I make regarding the integrity of historic timber frames?

The first concern would be the soundness of the existing frame. A careful inspection is necessary to determine if any damage (water, rot, insect,...) has occurred. I would suggest that you find a competent timberframer in your area to perform the inspection. Structural soundness would be investigated on the basis of the loads on the structure, and the species and grade of the existing frame.

The engineering gets interesting, as the frame was surely constructed long before building codes. I would suppose that the question then becomes if the structure is "grandfathered" or if it needs to be brought up to present standards.

I would also suggest hiring someone who can help you understand the historic layout system used when the structures were built. It will simplify the field survey work, and greatly increase the usefullness and accuracy of the documentation during conservation work.