What I ended up doing to solve this problem (or one similar) is in my "main" file declared my windows as having a global scope then was able to access them using that instance name directly. I only had to pull it off once or twice to get things to work, but it seemed to work just fine.
Basically like this:
In your main program file ( the one that the .plugin calls ) you initialize you window -
ajustedwindow = mywindowlayout()
Then any other windows can call it from-
ajustedwindow:SetOpacity( mycalculatedvalue )
It seemed to work just fine for me.