3) It is preferable to start with a blank drive. But...here's a suggestion:
You have your applications installed on the D drive, under a folder called 'Program Files', right?
Create another top level folder for these new application installs.
Call it 'MyPrograms', or whatever. It does NOT have to be named 'Program Files'.
This way, you can see what applications you had, install them under this new top level folder.
When done, simply delete the original 'Program Files' on the D drive.