FIRST - build a new BDC, let it sych up, then take it offline or ghost it, but leave it offline but accessible. If the 2000 upgrade causes problems, you'll need this server in it's unchanged state to restore your domain to a pre-2000 condition.
Then, pick the least-used DC, promote it to PCD, run the 2000 upgrade over the top of it, and continue upgrading your domain contollers if successful. You'll probably need to run Active Directory Connector for your Exchange servers to interact with 2000's AD. Your web servers should be unaffected until you upgrade them, which will include an IIS upgrade.