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where is the zip file supposed to be located? I haven't upgrade yet but it says it's downloaded. I want to extract it before I run it so i can share it here.
Nevermind, I see it's been shared already. Got beaten again!
Make sure all system apps are bone stock and present. If you have frozen/deleted stuff - unfreeze/restore it. Also if you have replaced stuff - put back the original. Update patches all files there - if there is something that does not match (altered) or missing - it will fail.
Being rooted does not bother the update, but you have to reroot after it is finished.
Not sure about clockworks, but root's superuser.apk stays. Additional stuff does not bother the update, but replacing or deleting existing will cause update to fail. If you open update file, you will see it performs patch on every single stock file in /system (as well as replaces kernel and boot loader).
I have upated mine while rooted, it worked fine, I had to reroot afterwards though. I don't have clockwork installed so I can't say about it.
I would recommend bringing the phone back to stock before applying the update.
You didn't do nandroid backup, did you? There is another option too. There is a D2G dump here in this forum - download the dump and restore the apps you deleted. Make sure /system/app looks just like the one from the dump. Make sure permissions are right too!
Dump is located in this post compliments to AngDroid.
Basically what you need to do is extract the files from the dump that you deleted and restore them back where they used to be and fix permissions. All can be acomplished with root explorer for example, or even easier - adb shell from the computer.
I think the rule of thumb with these blur phones is that you should not uninstall bloatware. You should use Titanium to freeze them, so that they can be restored when you need them.
I'd be interested to know if that works. It's supposed to restore a stock image, but with the apps deleted, I can't be sure. Here's hoping that if it fails, you get stuck at the M logo. If that happens, then you can just take it to a store and say the update bricked your phone. When you can't boot past the M, they can't tell it was rooted, and will probably give you a new one.