After some very good learning about what we were missing in our original in-place upgrade documentation, we have made some changes to the In-Place Upgrade instructions to help with some of the challenges partners and customers have been running into. The updated documentation for in-place upgrade is now live on TechNet - http://technet.microsoft.com/EN-US/library/jj733502.aspx (if you prefer MSDN - http://msdn.microsoft.com/en-us/subscriptions/jj733502.aspx). It will make its way into the next publication of the overall Upgrade Guide as well, but that takes a little more effort, so use the TechNet/MSDN documentation for this specific topic until you see a revision date on the Upgrade Guide after February 15th.
The major changes were around preparing your original database, getting a lot more specific about how many times to run the Setup utility and with which components selected, and also an AXUTIL command to be executed prior to exporting your fully upgraded model store so that it can be successfully processed during the live production upgrade.
Thank you to those partners who worked with us through the challenges to improve the documentation going forward.