[PLUG] grub problems or is it the noobie administrator?

[logical american]

Well, it looks like I shot myself in the foot good and need the 
assistance of a person intimately acquainted with grub.

I allowed Ubuntu to upgrade from 9.04 to 9.10 on my Toshiba laptop, but 
something went wrong with apt's autoremove configurator and some 
graphics library files got removed, so that Ubuntu would NOT boot into a 
GUI but stayed in run level 2.

I reformatted the hard drive and reinstalled Ubuntu 9.04 (with the idea 
in mind of updating the 9.04 with my backup disk) and everything went 
well. I then booted knoppix 6.01 in order to update all the folders on 
the harddisk (two partitions /(root) and /boot) and rebooted only to run 
in trouble during the boot sequence.  The UUID's didn't match and the 
load failed, Ubuntu opening a maintenance session.  (well, I had 
symbolically linked the wrong vmlinuz and initrd images in the root 
partition to the boot partition)

Realizing that I needed to run "update-grub" on both the /boot partition 
and the / (root) partition, I rebooted knoppix and mounted them as you 
would expect and ran "update-grub" and the command seemed to work.

However booting still fails, although grub does display all 3 initrd 
images, but says "file not found" after trying.  Is the MBR hosed?

I did follow the "fix" steps in Ubuntu, of

1. grub
2. find /boot/grub/stage1
3. root (hd0,0) (which step #2 finds)
4. setup (hd0,0)
5. reboot

but no such luck.

I mounted the CD run only session of Ubuntu 9.04 and tried to mount the 
partitions again, and run either the grub commands or the update-grub, 
but with no success.

What am I missing?   I could reformat the hard disk again and reinstall 
Ubuntu 9.04 but then I have a backup disk with 2 more changes in the 
linux kernel which will have to be updated.  I really would like to get 
Ubuntu 9.04 updated, then allow apt to update into version 9.10 again.

Any ideas?