Perl source is here: http://www.cs.stevens.edu/~gnajda/make_prepatcher/easy_prepatcher_source.zip (with BasePatcher.dat), http://www.cs.stevens.edu/~gnajda/make_prepatcher/easy_prepatcher.pl (without BasePatcher.dat, you can look at the source right in your web browser)

Both links include BasePatcher.dat, which is derived from any ManualPatch.exe from the website. Already having that instead of the script having to download ManualPatch.exe could greatly speed up the script if the ManualPatch.exe on the website is large.

If you want a patch for something other than the previous version to the current version, use make_prepatcher instead (see the spoiler below)

The security-conscious will realize that BasePatcher.dat goes directly into the patcher; they should download ManualPatch.exe from Nexon's website and let the script generate BasePatcher.dat if they don't trust where they got BasePatcher.dat from. A ManualPatch.exe can be downloaded on the main Nexon site at http://maplestory.nexon.net/WZ.ASPX?PART=/Downloads/GamePatches

The script was packaged in a .exe using PAR-packager.

I wrote a Perl script that generates a prepatcher, given any old manual patcher, the xxxxxtoyyyyy.patch file from the ftp, NewPatcher.dat from the ftp, and the patch notes (yyyyy.txt) from the ftp.

Download is here: http://www.cs.stevens.edu/~gnajda/make_prepatcher/make_prepatcher.zip

That contains make_prepatcher.exe. If you don't trust me, you already have a Perl interpreter, or you just want the source, download the source at: http://www.cs.stevens.edu/~gnajda/make_prepatcher/make_prepatcher.pl. The source was packaged into an executable using PAR-packager. I am placing the source in the public domain.

If and only if you choose not to use the .exe and use the Perl source instead, you will need the Perl interpreter, which you can download here: http://www.activestate.com/store/download.aspx?prdGUID=81fbce82-6bd5-49bc-a915-08d58c2648ca (download the x86 MSI). Once it is downloaded, install it. Again, you do not need to do this step if you are using make_prepatcher.exe

Now put make_prepatcher.exe or make_prepatcher.pl in a folder along with the ManualPatch.exe from any recent version (available at http://maplestory.nexon.net/WZ.ASPX?PART=/Downloads/GamePatches), the patch file for the new version (xxxxxtoyyyyy.patch) from the Nexon ftp, NewPatcher.dat from the Nexon ftp, and the patch notes for the new version (yyyyy.txt) from the Nexon ftp. (ftp://patch.nexon.net/Maple/patch/)

Run make_prepatcher.exe or make_prepatcher.pl (if you installed Perl, make_prepatcher.pl should be double-clickable). This will create a file of the form 00058_patcher.exe in the same folder. That's your prepatcher, run it and patch. I recommend backing up your MapleStory folder first, just in case it doesn't work.

Credit and thanks to maststef for explaining how to make a prepatcher!

You can also find the directions inside make_prepatcher.pl.