I have set up the fan circuit to run on iac1a it kicks on at my setpoint but will not shut off, even if the ecu is turned off. I have to physically unhook the relay or the battery. Is it possible to have this problem if the diode at the relay is backwards?

 

check the polarity of the diode.

 

Are you using a latching relay? That would be my guess if it kicks on at the right temperature but then won't turn off, even with the ECU off. How many pins are on the bottom of the relay, and does it have a part number?

There's also a chance you wired the hot end of the relay back into the trigger, in this case even when the MS shuts power off the relay coil will still get power from the output wire. If the relay isn't a latching model that'd be my next guess.