Compare your notes with the documentation https://docs.moodle.org/en/Moodle_migration. (It will jump to the latest, right now 3.0, version of Moodle. If yours is different, replace /30/ with your version.)
As Emma suspected, did you do an https://docs.moodle.org/en/Upgrading at the same time? That is never a good idea, because you will not know which step broke. Anyway, if you also upgraded, somehow it broke the https://docs.moodle.org/en/Repositories. For example, during a 1.9 > 2.x the dreaded https://docs.moodle.org/en/Legacy_course_files were created. Apart from that, I have no clue. I don't think you have Unix file permissions issue, since you can upload files. What are the URLs (the pattern) of those broken images?