Ok, this is what I did (and it worked):
1. Put all your wads into \wad.
2. Start 3ISOs several times, it will first recover all the necessary files/folders from the recovery-archive.
3. At some point it will process the first wad-file and then ask you to proceed using partitionbuilder (which already opened).
4. Except for the last "Browse"-button at the bottom, press them and navigate into the "make-iso" folder. The necessary files will be in there. With the last button navigate to "make-iso\sound" (opening.bnr should be in there).
5. Click on Build/Proceed/whatever-the-button-is-called, save the file (partition1.img) and exit partitionbuilder.
6. Wii-Scrubber will open up. Load the iso-file located in the folder above "make-iso" (I think it's called "Forwarder-ISO"). Then right-click on the first (and only) partition, select "unencrypted", then "load" and select the partition1.img located in "make-iso".
7. Exit Wii-Scrubber
8. The batch will proceed, a .txt-file will open up (don't know why
), just close it and you're done.
Inside the Forwarders folder you will find your files. The forwarder iso which you add to your (wbfs) drive and the XXXX.dol (XXXX meaning the game id) inside another folder which goes into sd/usb:\forwarders\platform\ (where platform is n64/nes/snes etc.).
This is it (basically)...