How do I move the window buttons back to the right for all users?

gconf-editor has an option to do this. Just right-click on a value you want to set for all users, and click "Set Default". PolicyKit will open and ask you for your password. After that every new user will have that value.

I don't know about install time, but when new users are created, the files from /etc/skel are copied to the new home directory. You could add a file

/etc/skel/.gconf/apps/metacity/general/%gconf.xml

with the contents

<?xml version="1.0"?>
<gconf>
<entry name="button_layout" mtime="1273173410" type="string">
    <stringvalue>:minimize,maximize,close</stringvalue>
</entry>
</gconf>

to /etc/skel.

Or you could create the perfect user-setup (let's name him perfectuser) on a new account, and replace

SKEL=/etc/skel

with

SKEL=/home/perfectuser

in /etc/adduser.conf.

That way, each new user you create would have the same configuration as perfectuser.

Maybe the install CD could also be modified in a similar way?

To change the setting for all users, you could write a script that adds

<entry name="button_layout" mtime="1273173410" type="string">
    <stringvalue>:minimize,maximize,close</stringvalue>
</entry>

to all /home/[user]/apps/metacity/general/%gconf.xml.

Download UbuntuTweak go to Window Manager Settings and click "Right"

Edit: I'm not exactly sure if this does it for all users but it is easy.