The process works for nearly everyone, so let's see if we can identify the issue specific to your machine(s).
First, the ETK descibes this issue: http://www.adobe.com/devnet-docs/acrobatetk/tools/AdminGuide/troubleshoot.html?highlight=f unctional.
The last bullet mentions that one could use the cleaner: http://labs.adobe.com/downloads/acrobatcleaner.html.
However, I'm not familiar with digital upgrades and don't know if you need parts of Standard to remain on the machine to upgrade to Pro. What exactly did you download? (list files/size).
First you are attempting to install Acrobat Pro XI over Acrobat Standard XI and it's throwing an error that you have a more capable product. While not the most elegant or even correct message IMHO what it means is that you can't install the same version of Pro over Standard. If they were different versions (ie. Acrobat Pro XI over Acrobat Standard X ) then it would work. There are good reasons for this installation error, but let us try to get you to the place where you can actually get the work that you need to get done accomplished.
You can use a virtual machine like VMWare, VirtualPC, Parallels, or Oracle VirtualBox to host another Windows instance and load Adobe Acrobat Pro on that vm. These are really the best way to keep things on the same machine and have both as separate usable installations. In all cases, you provide the Windows installation media. The price of the VM software varies from free to some reasonable prices. Your choice though.
VMWare is a purchased product Windows and Mac: http://www.vmware.com
Parallels is a purchased product for Mac only: http://www.parallels.com
VirtualPC is downloadable from Microsoft at no cost: http://www.microsoft.com/en-us/download/details.aspx?id=3702
Oracle VirtualBox is downloadable from Oracle at no cost: https://www.virtualbox.org
And one more thing... you need to contact Adobe Customer service because you should be using the full Acrobat XI installer with a full blown installer Serial Numberand not the upgrade installer with an upgrade serial number.