I also encountered a problem like this when trying to install, I think R3.1-rc1, to an external hard drive. In my case, the installer booted and installed Qubes onto the external hard drive. However, when it was time to boot from the external drive, although grub came up, as soon as the kernel booted, the USB port actually seemed to turn off (my external drive adapter has a separate LED to indicate the USB port is active. I saw similar symptoms as shown in your logs - the USB host controllers are detected, but the storage unit attached to the USB port is not. I believe some users have seen similar issues with USB-attached keyboards. This definitely was not a problem with Qubes R2 - I'm not sure I ever tried running from an external drive with R3.0.
My guess was that it was either related to USB 3.0, or the initramfs/initrd image is missing a kernel module needed to get USB storage to work. I took the cheap way out, and moved to internal storage. However, that's not much help for trying to run a Live USB.
Eric