Ok, I got my system working and I think I really understand the problem now.
1) I don't think it would matter what cloning software was used.
- Once you are broken it is very hard to do updates because the Windows Update Service is busted and that affects the ability to install things like MSU files, etc.
The new, bigger, Western Digital drive that I bought used advanced formatting and basically that means that the sector size is no longer 512 bytes. The old storage array driver for the motherboard component (in my case an INTEL piece of hardware) needs
to be current to correctly report back the disk status. Since you can't install a 'package' I ended up going to the INTEL website and getting the WINZIP download of the INF and other files needed to successfully to the update to the storage array driver.
I initiated that update with a right click on the specific item in Device Manager and told it to update pointing it to the folder I had unzipped the INTEL files. Once the bigger sector size is reported correctly, then Windows Update starts working again and
all is well.
Had I been smart, I could have done the driver update before the old drive failed and then the clone would have had the new driver and I would never have known I might have had a problem.
Those compatibility patches that are mentioned elsewhere for the advanced format drives are good too....but insufficient to make things work by themselves.
All the comments about saving the windows update files are good too...but not necessary if the driver gets updated before break Windows Update. It is a pain if you lose your update history and you have to paw through the updates you previously applied.
And the comments about registering various DLLs, etc are probably needed in some cases where the cloning really didn't go well.
Bottom line, get the storage array driver updated first.