Okay, so I can't really give the full details, but through a lot of trial and error I feel that I am close to getting things working fully.

I have one last problem, and it is driving me insane, because I know what I want to do but I can't.

I want to disable the filament cooling fan when the printer prints the HIPS support material, and turn it on only for the PLA.
BUT, when I disable auto-cooling in the HIPS settings, the fan stays on anyways.
I found out that this is because Slic3r uses the M106 or M126 (depending on GCODE flavor) command to turn on the fan during the PLA, but it never triggers M107 or M127 to turn it off when the HIPS starts printing. I also see that most of the time the fan is enabled during the layer change rather than when the GCODE switches between the extruders.

Is there anyway to make the fan turn off for one filament and on for the other? I need to be able to do this.