Odd, I tried to post a reply but it got eaten. Either way, I'm in the same boat, doing a similarly long upgrade. I'm pretty new to DNN, have taken over maintenance of our sites. I've read that modules must be updated separately - is that only specially-downloaded modules, or will the stock modules need upgrades too? Is there a listing of stock modules so I can see which of my modules will need an upgrade?

The only modules that are updated by the upgrade tool are admin/host modules, security modules (login and registration)  providers and the HTML module ... all other modules require manual updating.

The host menu - > Extensions page will show you a list of all the modules installed on your site - indicate which modules are In Use anywhere on your site - and also for DNN core modules - indicate if there is a later version available than the version installed on your server

Further more - on the Actions Menu dropdown of this same page - there is an option to Install Available Extensions  -  this will take you to a list of the module packages currently idownloaded and available to install.  After any upgrade it should contain a list of updated modules by version number.

Westta