I'm still getting the same error, even after the fixes.

$ ./multicd.sh
Made a link named ubuntu-alternate.iso pointing to ubuntu-12.04-alternate-i386.iso (version 12.04)
Made a link named i386.ubuntu.iso pointing to ubuntu-12.04-desktop-i386.iso (version 12.04)
Made a link named amd64.ubuntu.iso pointing to ubuntu-12.04-desktop-amd64.iso (version 12.04)
multicd.sh 7.0
Extracting ISO images with file-roller; will build multicd.iso; UID 1000.

Ubuntu alternate installer
Ubuntu (64-bit) 12.04
Ubuntu (32-bit) 12.04

Continuing in 2 seconds - press Ctrl+C to cancel
Copying Ubuntu alternate installer...
cp: cannot stat `/home/qyot27/MultiCD/temporary-mountpoints/ubuntu-alternate/ubuntu': No such file or directory