Plan C.
bilica:
...
I know that one possibility is to build linino from scratch. However, I have not managed to do it using a Debian 6 distro
(instructions : Building a custom image for Arduino YUN)
All you need is multible core cpu ( more is better), fast harddisk (scsi or ssd, faster is better) , a lot of memory ( more is better) , It would not fix error but failed faster then you could retry quick. once you build image. flash the new image.
http://arduino.cc/en/Tutorial/YunSysupgrade
During buildroot you could add additional packages as well as remove unused packages from image, plus put your config file or programming file at files directory under buildroot directory.
files/etc/banner for customer banner
files/etc/rc.local customer init script
files/www/index.php customer web file