Ok, so, the story so far has morphed a bit further based on some of the advice in this thread.
Again!
thanks so much everyone for your contributions.
So, I have implemented an RC filter on the ground side of the heating element between the element and the current sensor.
This has allowed me to gather current data suitable to my purposes and to run my experiments without further issue.
Its not a perfect solution, but it works.
I have also taken your advice and adjusted the supply voltage to suit the load, instead of capping the PWM in software.
the degree of element control I have thusly arrived at is sufficient for my needs.
I now have a different challenge, that I will post in a fresh thread under a new topic to distinguish it from this one. 
Thanks again everyone. I would consider this thread resolved for the purposes of moderation.