Hi Nathan,
Have a look at this youtube and Christpher Go's homepage. Theres a lot of useful info.
https://www.youtube.com/watch?v=8MeZhlV7p_Y
One thing he advocates is high gain for poor seeing.
I believe that 50fps is a sweetspot for Jupiter , and that there is too much cloud surface movement for videos over 90 seconds and that WinJupos can add what may be crucial derotation.
Follow Niall MacNeill on Astrobin and you'll pick up hints.
Do you use the Sky and Telescope things for GRS and Moons?
Thanks for data on Autostakkert settings / use. I'm not getting anywhere with it...
Good luck
GlennB