As mentioned here and here, bootrec.exe and bcdedit.exe have trouble functioning from a usb-booted WinPE environment. They tend to see the wrong sets of files and they also tend to break things (which I found out the hard way). As of yet, I have found no way to get them to see any file set other than that from which they were booted, IE not the WinPE environment. Booted from an actual disk, they work fine. It seems to be an issue with usb drivers in windows PE & RE from what little I was able to find. I have also tried gandalf50's (awesome) PE4 disk (found at http://windowsmatters.com/2014/05/15/standalone-win8-1update_pe-x64-or-x86-2/) with the same results.
I am a technician, though I still view myself as a novice. But I have built my own PE disks in the past and its not difficult at all. Why then does it seem impossible to get the functionality of these very necessary repair tools when the PE is booted via usb? I have found nowhere that describes a fix or any success stories or even anyone who has even attempted to get this to work. Personally, I run all my bootable tools from a single 250gb usb drive (setup with winsetupfromusb) and I greatly enjoy not being tethered to a CD/DVD binder anymore. Any help or knowledge on this matter would be greatly appreciated!
Edit: The bcdedit export operation fails. windows vista not booting The last post here contains a plausible fix. However, it requires that EasyBCD's iso caching method be used. I could re-do my huge drive with approx 30 bootable tools and this would work but its really a workaround in my mind. A creative solution regardless.