Thanks bigmck for the reply. Yes, that's what I'm going to do, just leave C as the OS and D as an additional storage drive.
After doing some research, I'm thinking it has to do with the Windows Installer Service, which for some reason was not starting. Perhaps something happened during the clone process or when I attempted to do a clean install. I ran tests on all the hard drives and memtest 3.5 on the memory and all seems fine there.
The only other thing I can think of is that I am using a wireless keyboard and mouse on that computer. I have read on other forums where others had problems trying to clone using a wireless combo, but I thought Acronis had fixed that issue.