So reading the thread here is what i now have to add.
I have since managed to get my temperatures to remain stable with autostart and stop functions. I went into the settings and made a few adjustments to the default cycles and heating settings (def not recommended and i will not post those changes as i wont be responsible for someone screwing or shortning the life of their extruder) followed by two autotunes once the system was up to temperature and extruding again.
The points i will add about my mod testing extruder...
I already had my motor on its own power source, to me the slight power drops and miniscule drop in rpm is unacceptable when aiming for industy quality filament, for most however the very brief .01+- variance this can cause is fine for home printing and will not cause any issues at all.
My fan is also set to come on along with my heater, i prefer the fan to be active from the start as activating it with the motor cause a slightly larger drop in power as they kick in, and the heating unit is better able to regulate when it has the airflow from the start not suddenly once up to temp.
Heater core and thermocouple placement.
Ive found that moving the heater core towards the back of the pipe coupler, and placing the thermocouple at the front, allows you more stable melting temps with the added bonus that it keeps your nozzle slightly cooler which helps which maintaining size on your filament as some heat is actually being pulled by the nozzle as its shaped and extruded. This is especially useful for pla until we get a combo water cooling and winding solution out into the wild and out of testing.
Coupling the auger to the motor... I am looking into alternate ways of achieving this as to me this is currently the weakest point of the extruders design. washers tend to slip or warp no matter how well or tightly fitted you have them. My current line of thinking is that squaring off the motor peg and using a socket wrench coupler may be the best bet for a snug fit.
Feed System for pellets/powders
For anyone who wants a more unattended feeding setup and isnt satisfied with a printed hopper extension.... You local Plumbing/Hardware store is perfect for this.. I am currently using a PVC plumbing pipe distribution system to feed my extruders from a large tank (can be built out of plexi, acrylic, and material that wont cause contaminents or you can use a fish aquarium) For powders i suggest a low rpm motor with fan blades attached installed in the piping in order to help facilitate flow of the powder and prevent clumping. This can also be used for pellets but so far hasn't seemed necessary.
Hope all this helps someone, and sorry for the run on sentences. Also anyone that wishes to add anything please do as this has been based off my experiences and im sure others have even better ideas and tips!