How To: Relocate the MIIS 2003 Database
This How To guide describes the process of relocating the MIIS 2003 database, named MicrosoftIdentityIntergrationServer from a computer that is running Microsoft® SQL Server™ 2000 to another computer that is running SQL Server 2000 with all critical data intact. Specifically, you will perform the following tasks:
• Stop the MIIS service, backup the MIIS 2003 encryption key and MIIS 2003 database.
• Restore the MIIS 2003 database to another server hosting Microsoft SQL Server 2000 Enterprise Edition.
• Uninstall and reinstall MIIS 2003 to point to the new server hosting the MIIS 2003 database.
More:
http://technet2.microsoft.com/WindowsServer/en/library/244b15d1-6363-42f0-b853-a62591b3fb021033.mspx?mfr=true

Can you have federated and non-federated sites in the same WSS site? If you set up WSS on the default site in IIS with one application configured as a federated token based app, does that mean that all other sub-sites have to be federated as well?
Options are:
1. Create a new web site that can be used for the non ADFS enabled sites
2. Install WSS which will install to the default web site. Create a second web site and configure the second site as a WSS site in sharepoint central administration. Now uninstall WSS from the default web site. At this point you can install other ADFS as well non ADFS enabled apps to the default web site.

Is the object always deleted from the metaverse when the last connector is disconnected (even if I am using ShouldDeleteFromMV to explicitly say leave object in the metaverse even if the last connector has disconnected)?
Yes, it is. A MV object requires a connector as justification for its existence. The sync engine removes automatically all MV objects without a connector. This is independent from the configuration of the object deletion rule.

How to monitor https traffic? Is there any IE plug-in available?
Look into:
http://www.ieinspector.com/httpanalyzer/index.html
www.parosproxy.org
http://www.fiddlertool.com

Is there a way to export MIIS flow errors to file to have a closer look?
You can use CSExport, there is a parameter to only export objects that show an error, '/:fe. CSExport is in the bin directory under the MIIS install folder. So if you ran 'CSExport AD ADErrors.log /f:e' from that directory, it should create XML file that only shows errors. Of course you would need to further parse this if you were interested in only the DNs.
http://msdn.microsoft.com/library/default.asp?url=/library/en-us/mmsdev/mms/hologram_xml.asp