You can keep PDF, CD, Zip or paper files. As long as you have something to show the IRS if they come calling. Obviously, you would need to keep paper signature files.
I don't know if you HAVE to give copies of 8879 and IL-8453 to client, but I always give copies of 8879 and WI WR-A to all clients as well as depreciation schedules and anything the would need to "build" their return if they would wish to take it somewhere else. I have had too many clients come to me with incomplete copies of their returns and the time lost in trying to gather information is invalueable.