Andrew,
First, you should never have begun cutting the project until you solved these issues. If you can’t solve the issues at the time of initial capture you will almost certainly be unable to recapture with any degree of accuracy.
Second, when you said, “Some tapes captured cleanly with good sync’ed sound and no video artifacts or noise. Others tapes had problems including a.)little square artifacts appearing on certain frames, b.) Entire stripes of video all askew, perhaps an interlacing problem, c.) audio out of sync., d.) no audio at all.”, you imply that you know this is a capture issue and that the tapes are all good. In fact, did you ever evaluate all the tapes to make certain the transfers from Beta were done properly?
DRW