Is there a way we can copy the source installation file from cPanel onto our server, and fix up a few things like headers/footers before the installation take place?

After you setup CPanel, you can login to WHM, and create a tarball copy of any skin you want, download it, and then edit the headers, images, etc...basically create your own skin.

Once you have done that, you can install that skin, and make it available to your customers.

Yes, custom cPanel skin, great for branding.

- Tomer

Yes, I realized that, but I would want it come pre-configured after the installation aside from the default theme.

The problem with is, cPanel is constantly updating their installer. So if you did so, after the initial install you could spend alot of time updating everything that has changed.

Bug Fixes, etc...

Yes, it is much easier to simply install cpanel configured the way they prefer it to be configured, and then update the configuration post-installation. You will avoid a lot of unnecessary hassles doing this.

If you all ready have clients that will be viewing this panel, then just explain to them that the new and improved panel will be on its way very shortly, and update it as quickly as possible.

You will save yourself time and effort this way, and it'll be better off in the end.