[Mark Spano] "specifically how to achieve perfect frame-accurate captures and edits to tape, and how to factor delay times for up/down/cross-conversions."
Since there's over a million combinations (format, frame rate, codec, environment, etc), this is pretty much futile. You will have to test
your config and your setup and find the right one. If doing a conversion (up/down/cross) you can pretty much settle on one frame delay.
[Mark Spano] "I feel like I've done this a bunch of times with the A protocol - but since this problem is intermittent, I am never sure if it's right. "
I'd suggest you read the manual in this regard as it really does have a very good explanation of this process. Now that Apple has made the manual available and searchable on the interwebs, here's the page:
http://documentation.apple.com/en/finalcutpro/usermanual/index.html#chapter...
Jeremy