Okay, it took some effort figuring this out, but none of the u3 customization tools that I found would do the trick.
Here's my little hack around it:
The only tool that could access the u3 partition in my brand new cruzer mini 8gb u3 drive was the newest version
of lpinstaller.exe from the sandisk website, however it automatically downloads the newest version from u3.sandisk.com during the installation.
So I fired up wireshark and discovered that the location of the download is u3.sandisk.com\download\apps\lpinstaller\isofiles\PelicanBFG-autorun.ISO
Next up, install a basic http webserver on your computer and get it running. Then create the folder structure in htdocs, and put your payload in isofiles as "PelicanBFG-autorun.ISO"
Finally, edit your hosts file c:\windows\system32\drivers\etc to redirect u3.sandisk.com to 127.0.0.1.
Now run the official installer and it should install your payload!
