I fixed the problem, but it's not a friendly/ideal solution.
You will need to use a Recovery Disk that you can create from another installation of Windows 8. It has to be 32-bit, otherwise the Recovery Disk can not be used on the Surface RT.
Boot into recovery mode and do a reset. I attempted a "refresh" where your files and apps are intact, but got an error stating the drive was locked. There may be a way to get around the locked drive, but since I didn't have any files that I needed
(other than the apps), I opted for the full reset.
Also, there may be ways to "fix" the BCD, using the command line in Recovery mode, but I didn't explore that option.
Perhaps, we can get some insight from Microsoft on ways of fixing the BCD without having to completely reset (i.e. fresh install) RT.
Once you have a clean install, the 8.1 update was not available in the Store until after I applied the 30 available updates. That whole process took about 5 hours.
The 8.1 update was successful on the 2nd attempt.
7 hrs just to get Windows 8.1 (not counting the 2 hrs on the first attempt)
~5-6 hrs to setup the Surface with all of the user accounts, email, apps
Overall, this is the WORST upgrade experience on a modern day OS.