OK, so here is a script that will change your PID on the fly between settings with the fan on and the fan off. I can make it so it uses more tunings if people want that (say a tuning for 0%Fan, 25% Fan, 50% Fan, 75%Fan, 100%Fan). Right now I have it set for two tunings, On/Off.
The script is called with the following, and outputs to "MultiplePID.gcode"
perl "/pathtoscript/MultiplePID.pl" "/pathToGcode/Input.gcode"
I can make it cleaner if people decide it is worth while, but I'm not really a Perl guy so until I get some input on if this is helpful to others I'm not going to stress myself.
Basically all this script does is search for M106/M107 and switches the M302 PID variables based on the fan being on or off. I can add more logic to search for M106 S*** for more PID tunings if needed.