Thanks for the replies on this thread.
I had temporarily forgotten that one of my co-workers recently spent a few months at a french monastery, where he participated in timberframe repair. He was able to shed some light on the subject and certainly came down on the 'patch where possible' side of the debate. I like Jim's comment that timber restoration is site specific and the same patch may not work in all spots. Also Emmet's comment on bolt diameter being a nominal 10% of post size seems sensible to me.
This frame will be disassembled and delivered to our shop, so it will be possible to have a good look at the timbers, and make better decisions. I also plan on drawing out the repairs and forwarding the drawings to the project engineer. Anyone else with restoration experience who would like to add to the thread, I would appreciate it.
Thanks again!