Hello Joseph,
I ran into the exact same issue (same stacktrace). Found
this bug report which helped me solve the problem. I just started the old server and went through all sites/organizations from the control-panel, deleting all bookmark-folders.
Perhaps not a good solution for you but we only had one site that had one single bookmark-folder with a few bookmark-entries so for us it was simple. We can always re-create the bookmarks manually if necessary. I guess it would also be possible to backup the tables
boomarksentry and
bookmarksfolder and re-create them using some fairly simple script.
HTH
Regards Thomas