I have studied and know how to fit everything else in.
But my main problem is I don't know where the front panel connections go.
My motherboard has some sort of all in one connector and the front panel pins add up to 14 pins but the last 14th one is missing (I'm not concerned about that):
You need to take a look at the original harness (usually 1 piece) on the old case and figure it out. Take a look at the dongle of wire that comes with the old case, and for each set of wire that comes out, which serves 1 function (1 LED or switch), trace it to where it connects to (position on the harness connector) and write it down (on paper with a diagram). Then you need to connect the new case connectors to the same positions that serves the same functions.
On the hardware maintenance PDF you linked to, on page 25, connector 11 is the connector you need to decipher based on the wiring harness that came with the old case.
LEDs are polarized, so if you connect them one way they don't light up, try swapping the position of the 2 wires (flip the connector).
Take a look at that photo i linked you to, I need to know what kind of front panel pinout my mother has, is it J18, JFP??
Please reply ASAP
Your photo-link doesn't work. It appears to be a link to your inbox, which I can't access. Your pin-out is proprietary to Lenovo. You just need to decipher it by looking at the matching (mating) harness that came with the Lenovo 520 case. Look at that harness, and figure out the pin configuration by tracing each function to a set of pins, and write down a diagram.
I'm not sure what J18 and JFP refers to. I didn't see them on Page 25 of the Hardware Maintenance PDF. The correct connector is connector #11 on Page 25 of the PDF (the motherboard might have it labelled differently, possibly JFP)