First start by putting a piece of plywood under the crate, over the old uneven wood floor, to create an even surface.
Second cut out a piece of cardboard roughly the size of the pan for the crate. This cardboard will go between the metal grate bottom of the crate and the pan, NOT inside of the pan.
Insert your cardboard noise buffer!
Insert crate pan and line it with a bed, matt, etc., for your favorite pooch. And he didn't fight us on going into the crate because it didn't squeak!