An assignment is an activity. Those could be old version assignments turned in by students and the 400 folders are student ID numbers with the contents being the files that were submitted by students. Think you'll have to look at an existing course to figure that out.
Lot's of potential issues if the backups were full backups from a 1.9.x version of Moodle.
When restoring a 1.9 course to a 2 Moodle must first convert the course to a 2 formatted backup and then it restores (or attempts to).
The max_packet_limit and open_files limit increase is what worked for me with a 'troubled' restore in the past.
So debugging turned on shows no errors ... or one just gets the 'white screen of death'? How about any hints clues in MySQL logs or apache logs or php error logs?
'spirit of sharing', Ken