If I flash stock and unroot via Nexus Root Toolkit... will this turn off usb debugging? My screen does not work after replacing the digitizer (it's just white...)

Before I go buying more parts, I'd like to eliminate software issues (apparently this can be caused by the device not wanting to accept new parts, this seems strange but I want to investigate it).

So, I would like to flash stock to bring it back to the beginning, and if it's still broken, it's still broken. Don't understand why the screen would have broken, since all I did was unplug it and plug it back in...

So, if I flash stock and unroot via adb, will this turn off usb debugging? If it does, I'll be done for as obviously can't turn it back on without the screen working...
Yes, the USB debugging would be found turned off.

The USB debugging settings are saved under /data, specifically mentioned under:


/data/property/persist.sys.usb.config
/data/data/com.android.settings/shared_prefs/com.android.settings_preferences.xml
/data/data/com.android.providers.settings/databases/settings.db


Because flashing a stock ROM would require you to wipe /data to avoid unforeseen issues, you would lose all the settings.

As you mentioned it yourself, flashing a custom ROM which has USB debugging turned on as default would be the best thing to do here. 

Note that if you're going to flash a ROM with Android 4.2.2 or above you would be required to authorize the debugging on Android. If you've a custom recovery, you may try my answer mentioned here and if you end up flashing a ROM with USB debugging turned off, this answer of mine may help.