Also, since Flynn was the only one able to create new programs, why couldn't he make a second copy of himself (CLU 3.0), with a sole objective to remove CLU and maintain the current structure of the grid?
Flynn had the master key that controlled the Portal, the only exit from the Grid. The key did not allow him to create programs, but the fact that he is a User allow him. And he is not an ordinary user, he is The Creator of the second Grid. (see : Why didn't Sam have the same powers as Flynn when he was in the Grid?)
Deleting Clu from inside the grid is not as simple as it would be from the outside. To get rid of him, Flynn had to reintegrate him, whatever that means, sacrificing himself in the process. Why it had to be done that way is a mystery, but it was supposedly the only way.
As for the creation of an other copy of Clu, I suspect the problem is that Flynn doesn't have access to the resources he needs to create anything new, since Clu took control of everything in the Grid and made sure Flynn could not access it.