Are you just doing a repair install over the top of an existing installation, or are you going the new installation route?
If you are just doing a repair installation, all your settings (shares, permissions) should remain intact (make sure you have a good backup just in case).
If you are doing a new installation, copying the info from the old to the new installation won't work.
Permissions (and to a lesser extent, the shares themselves) are tied to the SID of the computer that hosts the shares. Even though you are reinstalling the OS on the exact same computer, you will end up with a new SID.
Also, by reinstalling the OS, you are effectively removing the server from the domain which disconnects all users from the shares automatically. You will also have to remap all shares to the appropriate users (unless they are automatically mapped at log-on through scripts).