Here's what I'd do. With the server offline make a backup of the ioFTPD dir into a zip/rar just in case you edit/delete the wrong file. Then rename the ioFTPD dir to ioFTPD-old. Then extract just the ioFTPD.ini file from the original zip file you downloaded for your 7.0.3 release and stick into into ioFTPD-old/system/ioFTPD.orig or something like that. Grab a free file differencing tool like
WinMerge and compare ioFTPD.ini to ioFTPD.orig. This will show you any modifications you made to your current server from the default configuration which you now easily review.
Now extract the new ioFTPD release and edit the ioFTPD.ini as you want. Do go through it since there are tons of new features. By using WinMerge or just looking at the old ioFTPD.ini file you can see what you chose previously and copy things like Sections, VFS, etc over where it makes sense.
Trying to use WinMerge on the new ioFTPD.ini to your old will probably generate too many differences so that's why I suggested comparing against the old unmodified one.
Now that you have a new ioFTPD.ini file, just copy the /etc, /users, /groups, and /scripts dirs from ioFTPD-old. If you use nxTools you might need nxHelper, etc from the /lib dir as well. And double check what the old ioNiNJA required (like twapi maybe?), but I'd suggest upgrading ioNiNJA to the latest so you can just follow it's install requirements... Enable helpfile support for them in the .ini file as well
If you use merged directories in the .vfs file you may need to re-order them as I think we use the first dir listed instead of the last now but not many people use that feature.