Thanks to all for starting this thread and for all the great information. I decided I should finally make use of the XDA_UC tool.
I have been able to get everything automated from Configuring Wifi, Exchange /w Activesyc, all my Cabs, Settings (With Exporter), Copy2Root to move files, and keep my Stock listings.
I'm posting a couple registry settings below that were important to me to have.
The big one for me is having the phone not prompt to save a contact and disable the vibrate option when it connects.
If you want those settings modified they can be found below:
Items ending with 0 = Disabled , 1 = Enabled
"AddNumber"=dword:00000000 -- Prompts for Adding Contact
"ConnectingVibration"=dword:00000000 -- Vibrates Phone
"StylusOpenNote"=dword:00000000 -- Open Notes if Stylus is Pulled out during call
"RejectEnable"=dword:00000000 -- Enable Reject Caller with Message
Samsung Galaxy Note 3
Rooted via Kingo Root: AT&T Stock Rom, 4.3 - N900AUCUBMJ5