I think your approach is correct. I strongly recommend package upgrades over patch-based upgrades.
For best results, download the stock copy of OJS 2.2.1 and then use a tool such as diff ( http://man7.org/linux/man-pages/man1/diff.1.html ) or winmerge ( http://winmerge.org/ ) to see the changes made by the prior administrator. Local customizations can be readily managed by version control such as Git or Subversion, if desired. Always start from a place of the stock functionality, however, and evaluate any custom needs from there.