Lou,
Good Job! I recall many years ago, cutting a diagonal at the bottom right corner of a clipboard and fitting it with Velcro to hold it to the top tube and seat tube. I slid a sheet of graph paper under the main clip and used a small binder clip along the top edge of the clipboard to secure the plumb bob. The graph paper was an aid in making sure that you had a 90 degree angle for your measurement to the center of the seat lug. Of course, you want to make sure that the bicycle is sitting on a level surface, and the plumb bob will take care of the rest. Once you have established where the setback of the seat tube should be, it is easy to establish the saddle setback by running a string from the bottom bracket though the proper seat tube setback point and continuing on up to the saddle. this will be a good starting point for the center of the saddle rail.
Through my past experience, I have found that the saddle placement (seat tube angle) has a great influence on the riders optimal rate of spin. This is not due to the knee position over the pedal, but the angular change of the thigh as the pedals are rotated through their arc, and the relationship of the thigh angle to the hip and lower back. While I feel that it is a good idea to try to get your saddle placement the same on all of the bikes that you ride, this will not always be possible with large variations in frame geometry, particularly on larger frames.
I have a new web site http://billbostoncycles.com where I will be addressing many frame fit and design issues. The content is not there yet, but will be posted soon.
Bill Boston
Wilmington, DE