Your best bet maybe to start fresh and SBF your phone, it may take a few tries but if you follow these steps you should be in the clear. Once you have re-rooted you can restore a previous CWM backup.
FLASH 5.6.890 SBF (for a TOTALLY clean install for those with paranoia)
1: Download the 5.6.890 SBF file HERE
2: Download RSDLite 5.5 HERE
3: Extract the contents of the SBF file to a folder on your computer
4: Install RSDLite
5: Boot the Droid 3 into bootloader by holding both Vol+ & Vol- at the same time when powering the phone on
6: Select "AP Fastboot" and press Vol+ to select it
7: Select the XML from the extracted SBF file in RSDLite
8: Connect the phone, and when it says "Connected", hit "Start"
9: Wait for the phone to finish flashing, and booting (it will reboot a couple times, leave it alone, its supposed to!)
ROOT STOCK ROM
10: Install and run Petes Motorola Root Tools. Download it HERE
11: Follow the instructions in the app to root your phone