Using the "Timber Frame Joinery & Design Workbook" plus the peg & joint reports, your engineer should be able to arrive at load capacities for pegged joints. See also the recent article on computer modeling of timber frames. If it is a recycled frame, I have not seen too many (none first hand) that will on paper safely resist the code required wind or seismic load without some additional help. I have used reinforced masonry and concrete fireplace/chimneys, shear walls, hidden steel frames or tie rods, and stick-framed additions to dump lateral loads into. See also the Seismic design posts from earlier this year.
Good Luck