Interesting... whenever I get around to doing this, and that may be a while, I'll sync with the IAP disconnected, then check it again using Tee's and the IAP connected. I'll post here what I think.
I also noticed the comment on using vacuum gauges to sync the throttle bodies. Personally that sounds better to me than using anything with mercury. I assume the end result would be the same so are there any particular vacuum gauges I should use?