What exactly is the proper way to upgrade dopdf? No method has worked for me automatically. Every time it has been necessary to go to those System folders and remove the errant files by hand. Then the fresh install works.
Surely something has escaped my attention here.

Usually the upgrade should work just fine by simply running the new version and installing on top of the old one, then restarting the computer.
However, sometimes it's better to uninstall the old version first, restart the computer, and only after that install the new version.