The kernel in the ISO is /isolinux/kernel/sata. It gets copied and renamed in the installation process.
Replace that file with your custom one (name it "sata").
While there is no need to modify vlconfig.tlz for a changed kernel, your new /boot/System.map and /boot/config file should go in there.
To create a new vlconfig.tlz file, enter into the directory where you have the unpacked tlz file, issue command:
tar cpO * | lzma -2 >../path/to/the/file/vlconfig.tlz
Another option for a custom spin is the soon to be released VL6 Light Live version.
It can be installed to hard drive, modified, and made back into your own, personalized, tweaked, custom CD