your biggest problem is that "cdrom.iso". Your ks file is in that iso and that is not where it will be accessible.
As for the path to where you want your ks.cfg, you can put it anywhere, and just reference it during the boot process (or your isolinux.cfg if you want.). When you boot from the install cd and type "linux ks=cdrom:/ks.cfg" you are telling it to read the ks.cfg from the root of the cdrom. If you typed "linux ks=cdrom:/folderA/ks.cfg" you are telling it to read the ks.cfg from a folder "folderA". Also, you don't need to call it ks.cfg, you could call it ConfigA.cfg - just so long as you give it the correct path.
So, the easiest way, is get a correct Fedora install dvd or ISO, copy/extract all the files (including the hidden ones like you mentioned) to a folder. Then copy your ks.cfg to the root of that folder. Then bundle it back up using the mkfsiso you were using above. Burn to a DVD and boot from it. Put the command "linux ks=cdrom:/ks.cfg" and watch it work. Once you have that, then you can play with modifying your isolinux.cfg. I think you are basically correct with your isolinux.cfg modifications, I just haven't done that sort of thing in a while now, so I can't be sure.