how do you clean the cover scans?
With blood, sweat and tears. Also consumes one's soul.
Firstly in image editing software (for example Photoshop, Paint.net, Gimp. First being probably the best. Latter two free) removing possible moire effect (if image looks like it's made of little dots or "flowers") using gausian blurr with trial and error being careful not making the image too blurry/out of focus. It helps if your scanner has moire removal (aka derasterization or de-screen). Nearly impossible on some covers, I think PS2/PS3 being worst.
Then removing scratches and dust with various tricks which depend on software.
Then color balancing and resizing.
Remember: The better you get the scan the easier the edit is.
I suggest scan at 600DPI, finished cover 300DPI.