[Q] Problem while Rooting Xperia Arc

Hi,
I had rooted my Xperia Arc with eroot 1.2 but then got a bit carried away and moved some files I shouldn't had moved to my sd card and my phone started showing some errors like telling me the keyboard app has stopped or android.com.phone process as stopped.
Since that was happening I had to use pc companion and restore the original firmware.
Now, everytime I try to root it with eroot it fails. Any idea way I am sticking to what the tutorials suggest.
As I couldn't do it that way, I used flashtool 0.9.10 and doomlord script and manage to root the phone but strangelly it revert to its original state where it had files missing and started giving me notices that the keyboard process and android.phone had to be stopped and I can use sms because of that. '
Any ideas on how to fix this or way this is happening?
Already went on CWM recovery and cleaned everything and flashed the firmware several times but everytime the phone is rooted it reverts to this problem almost if he had some sort of recovery point to go to.
With stock firmware from Sony, everything is fine.
New to this site so please do excuse me if there is already any thread on this, I think there isn't.
Please help, thanks!

Someguyfromhell said:

Rooting again with Eroot. USB debugging on? Unknown sources turned on?
Which firmware are you actually trying to root?

You said you moved files to SDcard. What files? Did you try to move them back? If yes, did you set correct permissions (rw-r--r-- for apps)?

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Well, when I rooted the first time with eroot I had usb debugging on, unknown sources turned on and it worked but not now.
I am trying to root firmware 4.1.B.0.587 I can root it if I flash the phone and use doomlords script but not sure why the phone after being rooted restores to the point he was in August, with missing files and all. Mind that after I screwed up in August, I re installed the original firmware 4.1.B.0.587 via pc companion and all got back to normal and unrooted.
When I moved the files to the sd I moved several and phone was working ok till the next reset, when it started displaying the same error messages as now after rooting so I am not sure what files I moved, but I would say, at leats something like the keyboard apk.
It says the process android.phone.com stopped working and the same for keyboard so I can't access sms.
For the time being, I used pc companion to reinstal firmware 4.1.B.0.587 and it works fine but every time I root it, same mistakes reappear.
Shouldn't all data on internal memory be erased when I flash the phone with firmware 4.1.B.0.587 using pc companion? So, why do this erros reapear when I root it?
Thanks