So after many attempts to run a Coop game, I finally got one to virtually the end by playing FA Mission 2 "Dawn." After realizing that building experimentals causes desync (this had happened in previous unlogged games) I determined to get through one game without a single experimental.
The game was mostly going according to plan, except for the very end. After Princess Burke revealed herself as alive and everyone was all heartbroken and she and her Cybran boyfriend tossed nukes at each other the desync kicked in. We were close enough to the end that a blitz attack of 30-ish heavy gunships broke through and killed the Cybran ACU, which is the trigger to enable the last cutscene and end the mission, but when the Seraphim ACU appeared he didn't step out of the quantum gateway and the mission was ended when I closed the session.
Attached are the two logs I have available (there is no replay log for some reason?), which I submit in the hope that this bug can be narrowed down and eliminated. Note that the game.log file is a highly edited copy, removing over 800 megabytes worth of the "warning: snd: xact3dapply failed." notification.