Keyboard setting will be overwritten by the knoppix-autoconfig script which is run on boot. The best way to get your keyboard as you want it is to use the correct cheatcodes, and even add a new lang section to knoppix-autoconfig if you need to! Editing the isolinux.cfg will let you set the "default" language (i.e. change lang=de to lang=ie) or you can set the keyboard, xkeyboard and kdekeyboard cheatcodes. If no lang= cheatcode is right for you just add your own lang= section to knoppix-autoconfig, adapting an existing language to what you need.

As for your notes file appearing under /KNOPPIX, this is normal. The remastering process does 2 things, first it creates the large compressed system which is mounted as /KNOPPIX when you have booted up, then it creates the cd image which includes this file along with the kernels, initrds, isolinux and any other files you can see if you just browse the cd. When you put your notes file in / in your remaster you are actually putting it in the root directory of the large cloop file, not the root directory of your booted knoppix system. If you REALLY want your notes file to be placed in the / directory, then you would need to add it to the initrd files (which are gzip compressed loopback filesystems, gunzip and mount -o loop), but probably you want it to go into the users home directory? If you want it in the home directory then you would add the file to the appropriate place in /etc/skel.

As for the KDE and background, you again need to be making your changes in the right place (probably /etc/skel), the remastering process wipes the users home directory (it is populated afresh each boot from /etc/skel) and I suspect this is all you are missing out on. If you are making the chages somewhere else then let us know where and I'm sure someone can point you in the right direction.