Unless you have changed files that shouldn't be changed (i.e. files that are included in the release) you can simply follow the upgrade instructions of the
upgrade manual which should be far easier than what you describe below.
I'm normally using the Git repository which means an upgrade is a matter of executing one command (and you can also use the stable branch which only contains stable releases if you don't want the development version). I think that should also be possible on Windows and at least on Linux it's also easily possible to first create a separate Git copy of exactly the version that you are using and then copying just the .git-directory (which contains all the version information) to your current DokuWiki installation. That way it is possible to migrate non-git installations to git and then do the upgrade using git. I haven't used Git on Windows yet but as even Visual Studio
has got Git support recently I think it should work quite well.