I've been doing some reading on this since my Flyin Miata Stage 2 fans are coming in this week. I have a MSlabs MS3 basic, I'll probably wire in the relay to switch between two PWM settings for AC.

 

Quick update for anyone who finds this in the future. If you have an MS3 you are in luck as the most recent alpha firmware added PWM fan control that should play nice with AC. I`ll give it a shot this summer when the weather heats up and some of the bugs are worked out of the alpha firmware.

https://www.msextra.com/forums/viewtopic.php?t=77253

 

Have you had a chance to tinker with this yet? I'm installing the stage 2 kit and trying to decide if I should update to 1.5.2 alpha or stick with 1.4.1 and use the FM workaround with the potentiometer. Seems like those are the 2 least complicated options?

 

I believe you can make custom PWM outputs through tuner studio. The normal fan out put is just on and off. Or like others said just use a potentiometer to reduce power draw or just get the fan brain kit from FM and use a hose splice to get the sensor in.