Just downloading from the website and running the installer will work. You’ll want to be sure and select the Scrivener directory where you installed the previous version.
I also encountered this error (if my “helpful” answer didn’t make that obvious). Here are some hopefully relevant bits of info for my sitation:
I’m running Windows 7 (64 bit)
I do not have direct administrator rights; When installing software (and doing other tasks), I must enter a separate administrator username & password when prompted by Windows.
I too installed in a custom location (a second hard drive).
Under Control Panel->Uninstall or change a program, Scrivener is not listed at all.