Coop, full diffs on every incremental change. The only changes in the definitions were a couple of tables where the auto increment value was changed. Otherwise, minor data changes.
I think I've given up and moved on. Next step, recreate the structure and import data in chunks as small as I can make them without breaking relationships and try to either get all data in (problem remains a mystery, but I'm over it) or I isolate where the problem is coming in.