I went through this update fiasco with two different Atrixs, One unlocked, one locked.
Unlocked device:
I could not get the OTA update to work no matter how "back to stock" I was.
I kept receiving Failed to Boot 2 errors and could only solve them using RSDlite.
I also received a Failed to Boot 1 when using the auto-update tool and RSDlite again was the only solution.
Each time I used the pre-unlocked 4.5.91 sbf to fix.
After returning that device, for unrelated issues, I got a brand new, locked, device.
I applied the OTA update before unlocking.
Then I flashed pudding.sbf and got:
SVF message: 105:1:2
Failed to Boot 0x1000
I thought I was done for.
But after trying many different button combos I was somehow able to get to fastboot.
I think it was holding vol up and power while inserting the battery that got me into fastboot.
From there I tried to flash different 4.5.91 partitions starting with boot but it kept failing.
So, I proceeded to finish the unlock by, fastboot oem unlock.
That got me into a bootloop and I was able to reboot into fastboot the normal way where I then installed the stock 4.5.91
system and boot images.
I was then able to boot into 4.5.91.
If you get to this point I recommend waiting for a fruitcake or trying out
NottachTrix.
It was a real pain to get the update flashed and booting, more trouble than it's worth unless you plan on ripping it apart. I believe it's because there were apk patches opposed to full apks. Also boot patches that I think checked for an unlocked bootloader. But I'm not sure about that.
I hope this helps anybody who may find themselves in a similar situation.