The cooling fan relay triggers from a ground on (black/blue?) cable from ECU pin 15. On pre 2014 models this pin was unused but the sub loom supplied in cooling kit add it, matching later models which had cooling fan ex factory. The firmware flash presumably activates pin 15 and I would blame lack of this upgrade but for the fact you say the cooling kit was working previously. Given cooling fan works when its relay coil contact 85 is grounded this only leaves the sensor and relay trigger wiring plus sensor itself as possible faults. Since you have already had problems with pin 15 ECU connection I would double check that as well.
S & S provided Pro-Tune software to read ECU parameters via a USB socket on your car. Hopefully others current with this software will be along to give instructions, or you can download and read the manual for it
here.
