I'm not sure what you mean when you say the case wires don't match the diagram. You might mean there is already a plug on the end of the wiring, and this plug doesn't match the board header. If you're reusing the case from a name-brand machine like a Dell or HP, this is possible. They often get custom versions of motherboards made, and their front panel connectors are usually a nonstandard layout. On the other hand, in a generic retail case, the front panel wires normally have separate connectors on the ends for the switches, indicator LEDs and any front panel USB and audio jacks.
This is the front panel header diagram I found in the manual for your board (I looked at version 2, but the connections should be the same if yours is a different version):
This board has an Intel standard layout for the header. If your wiring has separate connectors, the start (power) switch wires will plug onto pins 3 and 4. I have never seen a retail case come with anything other than a two-pin plug on the end of the power switch.
If you are dealing with a custom plug on your case's wiring, what you can do is remove the pins from the housing. They almost always are held in by a plastic tab on the connector shell that engages a tang on the pin. Use a thin object like a small flat-blade screwdriver or a knife tip to lift the tab and you can slide the pin out. Insulate each pin with small-diameter heat-shrink tubing if you have it, or a layer of electrical tape. (I prefer the heat-shrink tubing, which is neater and more permanent.) Then you can put each pin over the corresponding pin on the motherboard's front panel header. Unless the pins are very loose, they will stay in place by friction. I often use this technique when salvaging a case.
As for the CPU fan, be sure you have the connector over the right pins. Here is the diagram from the manual:
You might need to rearrange the pins in your fan power connector if they don't line up correctly. This layout looks a little strange.