No /EFI/Boot is NOT on the persistent partition. EFI partitions must be the first primary partition on the drive. It MUST be formatted fat32. Then you can follow the above instructions. The EFI partition can be the same partition you write the iso files out using win32 disk imager. I have a 16GB flash drive partitioned liked this:
/dev/sdc1 primary partition formatted fat32
/dev/sdc2 primary partition formatted ext4

I used windows 7 diskpart to clean all of the data and partitions off the thumb drive. I then created the primary partition and sized to 4GB. I used win32 disk imager to write out the iso. I followed the above instructions to make it EFI bootable. I then EFI booted from the thumb drive. Once in Linux I created the second partition and formatted it ext4.