Here is an update - a reboot of the Shield and it is now broken again. I had to repair the hub to get it to work. Also, the android app is pretty terrible. I am constantly having to force stop it and reopen it to get it work properly.
I have determined with 100% certainty why it was not working - For whatever reason the app never properly downloaded the remote codes to the hub any of the dozen or so times I tried adding the nvidia shield. However I have managed to get it working using the following steps:
1. Removed the NVIDIA SHIELD device (device is all caps in the app when selecting the Nvidia logo from the hot brands list.
2. Add new device - instead of selecting the nvidia logo use the quick search to enter brand - Nvidia (NOT NVIDIA SHIELD although it might work 1st time.. I'm not starting over to find out) for device model I entered shield
3. This adds a new device - Nvidia (not NVIDIA SHIELD) - this is an IR device but it does download all the codes. This device will NOT control the shield.
4. REMOVE nvidia device
5. ADD new device - again use the quick search - Nvidia but this time select NVIDIA SHIELD. This time (for the first time) it actually downloaded the bluetooth device codes so the remote keys were not greyed out in the app.
At this point I was able to recreate a Watch Shield activity and properly configure all devices. Everything is now working correctly. I will not call it a success until I have a working remote for a week without any issues/dropped remote codes/etc but I am not cautiously optimistic.