RE: CRM 2015 Installation Error: The Website does not exist
We too came across this issue in several environments and after reaching out to Microsoft support were able to identify the root cause of this issue.
Here is the description of what causes the error and how to fix it.
By default when the MS Dynamics CRM application is installed it will create a Site ID in IIS, the next one available. So if Default Website is 1, and no other sites present in IIS at time of initial install MS Dynamics will take the Site ID of 2.
In our case because we run multiple sites we like to change the sites ID's to match whatever port number we use for a specific application. If that setting doesn't match what was recorded in registry at the time of install, then you will get this error of "Website does not exist" because it's looking for the site to upgrade based on the Site ID.
To fix this issue go registry HKLM\SOFTWARE\Microsoft\MSCRM\website
Change value from /LM/W3SVC/2 (example) to match whatever Site ID you have for Microsoft Dynamics CRM site in IIS. In this example we use port/site id of 12345 so we will change the value to /LM/W3SVC/12345
After that upgrade to 2015 runs without the error.