Upgrade and Install fails after first boot. Then I am unable to repair

I don't know if anyone else has experienced this?
I've experienced the aqua screen of death with the Upgrade option and was unable to resolve it, even after trying the APE removing technique.
So, I decided to restore back to Tiger 10.4.10 (thanks to Super Dupering prior to upgrade) and try the archive and install option. All appeared to go well, installed fine, allowed me to login and run all my apps. But, upon doing my first reboot after the 'sucessful' install the system just hangs at the gray screen. I tried using Disk Utility from the Leopard DVD, but it's unable to repair permissions.
I got this error message: 'The underlying task reported failure on exit'. Tried many times, I also tried the /sbin/fsck -fy in single user mode.
I tried booting into DiskWarrior 4's. Once in DW4 I ran the Repair function there... Here I got another error message.
This error being: 'Error -9997'.
OK I thought, something random must have happened. Soooo I restored to Tiger again and ran the Archive and Install option once again.
I'm am again experiencing the exact same problems with freezing gray boot screen and the inability to repair permissions (all after doing my first boot after sucessful install and login/opening of many apps)
Please please please can anyone she some light on this problem???
I'm going to try one more option:
Upgrade after I've disable all startup options and removing anything to do with APE....
I will report back!
This is really really crap Apple, I can't believe I've spent £85 and probably 15 hours on this sloppy release. Utterly disapointed

Just me it seems then....
Right, I think it's finally resolved, only after the fifth time. I've now rebooted twice and so far so good.
There was a new message when I powered down for the first time, something along the lines of:
Please wait while your Boot Caches are updated.
This seems to be a reasuring message, I feel almost confident in restarting again.
I upgraded using the following method:
1. Disabled ALL startup items (System Preferences>Accounts>Login items)
2. Removed all traces of APE (Application Enhancer) using Finder:
/Library/Preference Panes/Application Enhancer.prefpane
/Library/Frameworks/Application Enhancer.framework
/System/Library/SystemConfiguration/Application Enhancer.bundle
/Library/Preferences/com.unsanity.ape.plist
3. Repaired Permissions
Right, before I perform a new backup I think I'll see how she runs for a week, so I'm sure the boot problem is definitely gone.

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