There's a quick and easy method of installing Ubuntu (or any derivative) from a pendrive: isohybrid.
It's a tool which is part of the syslinux package.
just install it, then type
where FILENAME.ISO is your iso file. The md5 checksum will change, of course.
Then, you can just write your modified iso file to a pendrive:
where sdX is your pendrive device name. Pay attention!
I wonder why the standard ISOs aren't already patched with this. Or maybe they are and I didn't know it?
dd if=FILENAME.ISO of=/dev/sdX
Hope this helps