Thought you would say that! .
This will preserve your app and data settings.
If you had custom recovery installed just reboot into fastboot and flash the recovery of your choice. example: fastboot flash recovery ,recovery image name>
If you want to reroot, download a superuser zip file to your device, reboot back into your custom recovery and then install the SuperUser zip of your choice (i.e. chainfire's SuperSu)
Hopefully this is straightforward and self explanatory