Sam,

I believe the first sentence in your inquiry answers your question. Connecting new framing to old is both complex and challenging, particularly when you are dealing with such a historic structure. I have seen work done both ways in old and new additions to existing frames. Most often the completely free standing approach is used when moving an old frame and using it as the addition. This is fairly common in old barns.

Although it is by no means incorrect to modify the existing timber frame, this kind of work is best done by someone with a great deal of experience. If you intend to do the work yourself, I would recommend having someone review your plans to ensure the free standing structure is rigid enough to function correctly.

One other piece of the puzzle is wether or not the new frame is true to the style and form of the old. You may not want to use the scribe rule layout system that was used originally, but I would strongly recommend using a historic pattern in the design of the new frame. Karmic balance and all that.

Good luck and work safe.

Rudy