Thank you so much Markus!
I realised that I had missed out 'uboot-custom.txt' the first time, I put that on the USB and re-ran the installer using 'run recover1' and now it's all working beautifully, now to get writing to them NTFS partitions!

Thanks
P.S.
Is there any way to have the OS installed to NAND, but have some programs installed to an SD card while still using Apt-Get to manage the packages?
Glad you got it working again.
apt-get ntfs-3g to add your NTFS functionality.
On your final question:
Software installation spreads files throughout the filesystem. Let's take samba as an example:
dpkg -L samba/.
/usr
/usr/bin
/usr/bin/eventlogadm
/usr/bin/smbstatus.samba3
/usr/bin/smbcontrol
/usr/bin/profiles
/usr/bin/tdbbackup
/usr/bin/pdbedit
/usr/sbin
/usr/sbin/smbd
/usr/sbin/nmbd
/usr/sbin/mksmbpasswd
/usr/lib
/usr/lib/samba
/usr/lib/samba/vfs
/usr/lib/samba/vfs/recycle.so
/usr/lib/samba/vfs/audit.so
/usr/lib/samba/vfs/extd_audit.so
/usr/lib/samba/vfs/full_audit.so
/usr/lib/samba/vfs/netatalk.so
/usr/lib/samba/vfs/fake_perms.so
/usr/lib/samba/vfs/default_quota.so
/usr/lib/samba/vfs/readonly.so
/usr/lib/samba/vfs/cap.so
/usr/lib/samba/vfs/expand_msdfs.so
/usr/lib/samba/vfs/shadow_copy.so
/usr/lib/samba/vfs/shadow_copy2.so
/usr/lib/samba/vfs/xattr_tdb.so
/usr/lib/samba/vfs/streams_xattr.so
/usr/lib/samba/vfs/streams_depot.so
/usr/lib/samba/vfs/readahead.so
/usr/lib/samba/vfs/fileid.so
/usr/lib/samba/vfs/preopen.so
/usr/lib/samba/vfs/syncops.so
/usr/lib/samba/vfs/acl_xattr.so
/usr/lib/samba/vfs/acl_tdb.so
/usr/lib/samba/vfs/smb_traffic_analyzer.so
/usr/share
/usr/share/man
/usr/share/man/man1
/usr/share/man/man1/smbstatus.1.gz
/usr/share/man/man1/smbcontrol.1.gz
/usr/share/man/man1/profiles.1.gz
/usr/share/man/man8
/usr/share/man/man8/smbd.8.gz
/usr/share/man/man8/mksmbpasswd.8.gz
/usr/share/man/man8/tdbbackup.8.gz
/usr/share/man/man8/eventlogadm.8.gz
/usr/share/man/man8/nmbd.8.gz
/usr/share/man/man8/pdbedit.8.gz
/usr/share/doc
/usr/share/doc/samba
/usr/share/doc/samba/diagnosis.html
/usr/share/doc/samba/README.Debian
/usr/share/doc/samba/copyright
/usr/share/doc/samba/NEWS.Debian.gz
/usr/share/doc/samba/README.build.gz
/usr/share/doc/samba/changelog.Debian.gz
/usr/share/lintian
/usr/share/lintian/overrides
/usr/share/lintian/overrides/samba
/var
/var/lib
/var/lib/samba
/var/lib/samba/printers
/var/lib/samba/printers/COLOR
/var/lib/samba/printers/IA64
/var/lib/samba/printers/W32ALPHA
/var/lib/samba/printers/W32MIPS
/var/lib/samba/printers/W32PPC
/var/lib/samba/printers/W32X86
/var/lib/samba/printers/WIN40
/var/lib/samba/printers/x64
/var/spool
/var/spool/samba
/etc
/etc/ufw
/etc/ufw/applications.d
/etc/ufw/applications.d/samba
/etc/logrotate.d
/etc/logrotate.d/samba
/etc/init.d
/etc/init.d/samba
/etc/cron.daily
/etc/cron.daily/samba
If you expect to "install" your applications exclusively to the SD card, and not to NAND, then you would have to mount (according to the above list) at least
/usr,
/var and
/etc on the SD card. And if you were to do that, you really might as well put the OS on the SD card. I suppose you could put just /usr and /var on SD, you could even have some funky linking mechanism so that your files in /etc pointed to the SD card, but what would be the benefit?
If you were to manually install applications - and this would be most suitable to simple binaries that don't require documentation or configuration files - then you could far more easily place them on your SD card, and if necessary modify your path to include the relevant location(s).
The way we see the SD card issue is this:
Flash memory wears out. That applies to both the internal (non-replaceable) NAND and external USB sticks and external SD cards. Of those 3 possibilities, we think we'd probably want to use the USB socket for some hardware add-on, which means we can choose between NAND and SD card. Well, we can obtain an SD card with several times the capacity of the NAND for a tenner (and you can buy them from our shop too). If the card wears out, we can dispose of it and buy another. If the NAND wears out, we have to buy a new plug. Since the performance on SD card is just fine, we prefer the SD boot option. Furthermore, if you have (say) 3 SD cards you could allocate them for:
(1). Media Server
(2). Development / kernel compilation etc
(3). Testing new Media Server builds
You can reboot and swap an SD card in about 60 seconds - that's not so easy to do on a desktop with IDE and SATA drives. Each card, with O/S and key data can be backed up / snapshotted (to an external USB or eSATA device) at around 1G per minute (by booting from NAND and using dd).
So we think that a simple SD card boot, with O/S and data all on the card, is the way to go.