Have you tried to install steam onto flash drive itself? You may need to do that from another computer.
Then:
create a folder in flash drive steam directory named steamapps, then create a folder called "common" in this folder.
Copy the Faster Than Light, Super Meat Boy, and Dungeons of Dredmor NCF files from steamapps to the flash drive steamapps.
Copy the Faster Than Light, Super Meat Boy, and Dungeons of Dredmor folders from steamapps\common into your flash drive's steamapps\common folder.
that might have the exact same effect as just copying the whole steam folder (minus steamapps of course) but I think it's worth trying.