PWM signal through a mosfet
Insight on how to get a PWM signal to flow across SD would be greatly
  appreciated


The first battle is keeping the MOSFET turned on when source is dancing up and down due to the input signal - you have to ensure that the gate voltage is significantly higher than the maximum voltage at the source or the MOSFET may start to switch off.

The second (and harder) battle is keeping the MOSFET turned off when you don't want a signal to pass. I'm assuming an N channel device in this answer.

If the source input is a PWM signal (say between 0 V and 5 V) then you have to ensure that the gate (off) signal is the same as (or more negative than) the source signal. 


  I attempted this and when i apply my PWM signal to S and open the gate


No, an open circuit gate is a bad idea - it will float to some value (because it is very high impedance) and either turn on the MOSFET or cause some manner of feedthrough from source to drain.

Tie gate to 0V to turn it off but, then you have the problem of the internal parasitic diode inside an NFET: -



It's hard to find an NFET (or PFET) without one.

So my recommendation is use an analogue switch (simplified diagram): -



This overcomes the body diode problem because the "body" isn't joined to the source.