I just went through something similar like this last week, what a pain in the A$$.
Not entirely sure if this will fix your issue, but hopefully it'll help some how.
I ended up having to manually install galaxy nexus driver so I could sideload a ROM since I formatted my internal storage to test out this new F2FS BS... Anyways.
First you'll need to download and unzip "universal naked driver 0.72" Google it.
Now, without your GN connected open device manager and THEN when you plug in your GN to your PC you should see it pop up in the portable devices section.
AND also under other devices there should be "galaxy nexus" right click on it and click "update driver software"
Click "browse my computer for driver software" select the unzipped universal naked driver folder, click next and click "install this driver software anyway"
Now it should show "Google galaxy nexus ADB interface" in device manager under Samsung Android Phone.
Reboot GN into bootloader
recovery (if you have a ADB supported recovery eg. TWRP 184.108.40.206, and enter ADB mode)
Now there are 2 ways to do flash an Android OS, some may find 1 easier then the other:
download/install "Wug's Nexus Root Toolkit aka NRT v1.8.3.sfx"
Run NRT and it'll instruct and guide you through the steps required and whatever is needed to continue, eg. Select device, download TWRP 220.127.116.11...ETC.
Download/install ADB setup 1.3
I found this method a little more simpler.
Open the folder you have your ROM/gapps zip files saved on your PC, hold down shift key and right click on the folder, click "Open command window here"
Now in the command window type in "adb sideload XXXXX.zip"
XXXXX = COPY/PASTE the ROM file name. Eg. 20140615PA443RC2.zip
Press enter and now it'll flash the ROM onto your GN.
Repeat the same steps for gapps/kernel zip files.
Reboot your GN and enjoy.
I'm still loving running ParanoidAndroid Jellybean 4.1.2.