Sony say "Sorry!", to all their screaming fans on their Blog on Monday, and released new versions of the v3.41 files which they claim will fix up your bricking machines due to user-upgraded HDD's.
Not sure how this will fix those stuck in a loop at 99% since you can't get into the "recovery menu", because how you going to tell the PS3 to look for this new files on a USB stick if you can't get into the "special menu".We have released a new version of system software update 3.41 with a very minor change (the version number does not change) on August 2. If you are experiencing such symptoms when replacing the HDD of your PS3 system, we kindly ask you to use the latest data and try again. We apologise for any inconvenience this may have caused, and appreciate your understanding and continued support.
The only way, I been able to unbrick those 99% machines, is to open up the system and remove the small 3volt battery which holds info like clock, update flag, hdmi setting, etc.
Sadly, the funny thing is, all the bricked machines I see at my shop, had original Sony supplied HDD's, nothing "upgraded" about them. -- Oh'well!