[Xperia Arc Themes and Apps] Joe136:
Don't know if you still need help or if you already repaired your phone:

You said, you have wiped your phone so you can use the Repairinstallation of the PC Companion (Main -> Support Zone -> Update -> Repair Phone).

For all other people, there is a second way to rescue the configs of the Userapps (not the system configs like SMS, Contacts and Calendar):

Google: "How to Create an FTF file of Your Xperia ICS Firmware" (Vijay's Tech Encounters)

But in point 6, select only 'system'-entry in the list, flash it with Flashtool, root the phone and restore the Android ID or save the settings with Titanium and wipe.

I have bricked my phone too, the problem was that I couldn't change the privileges after replacing, the system throws toooooo many errors to interact with the phone. I have used the script below at second time to install it correctly.

Unpack the "system"-folder to SDCARD, place the script below into this folder and start the script in a Console-App with sh <scriptname> (or su sh <scriptname>), at last restart the phone.

source=${PWD}/
target="/system/"

echo Mount system as rw
mount -o remount,rw -t $(mount | awk ' /\/system\/* /{ print $5 " " $1 " " $2 }') || mount -o remount,rw /system

# Apps
curr="app/Conversations.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/GenieWidget.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/Home.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/Phonebook.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/QuickPanelSettings.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/SemcPhone.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/Settings.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="app/SystemUI.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

# framework
curr="framework/android.policy.jar"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="framework/android.policy.odex"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="framework/framework.jar"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="framework/framework.odex"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="framework/framework-res.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

curr="framework/SemcGenericUxpRes.apk"
echo Install: $curr
cp "$source$curr" "$target$curr"
chown root.root "$target$curr"
chmod 644 "$target$curr"

The script mounts the SYSTEM partition as writable, copies every file and sets the privileges (needs busybox).