I'm assuming you have a 05-09 car + Roush M90 blower + 2.49" pulley ? How are you measuring cyl head temps / coolant temps / tranny temps.. while driving ?
Oem T stat is 190 F. On my 2010 auto with M90 + oem 73mm pulley ( 2.875).... sitting in the driveway on idle, coolant temps will creep up to 204 F, then low speed fan kicks in. Coolant temps slowly drop to 194 F, then low speed fan shuts off. Then it creeps up again, and the cycle just repeats itself over and over. I had mine tuned by VMP, and they unlocked the SCT-X3 so I can tweak all sorts of stuff, including the low and high speed fan thresholds.
Low speed fan is set at 204F, and high speed fan is set at 212 F. I can adjust both of em a lot lower ( and higher). I can also set the high speed threshold to a lower setting than the low speed threshold.
My cyl head temps are typ 6-8 deg F hotter than the coolant temps, this is normal. Cruising on the hwy at 45-70 mph in OD, coolant temps sit at 198 F, CHT temps sit at 204-206 F. Auto tranny temps sit at 170 F. Fan is OFF. This is all with the oem 190 F T stat. With car moving, you have air passing through the grilles.
Going to a lower T stat only works, if you also reduce both the low + high speed thresholds. Even then, that only works around town..and cruising on the hwy in OD.
On a road course, with sustained high rpm, wot runs, blower on....and esp with that 2.49" pulley, things will get hot..and fast..and stay hot. A lower T stat..and mating lower fan thresholds won't achieve anything. With the 2.49" pulley in there, the M90 is well beyond it's limits..and blower eff is really piss poor at higher rpms. IAT's rise, and everything gets hotter.
My auto tranny temps would rise from 170 F to 200F in just 5-8 secs with M90 on. I installed a 2nd auto tranny cooler in series with the oem unit. Now auto tranny temps only rise to 170-171 F. That problem solved.
The 2010-2012 cars have this semi useless upper grille that impedes air flow. Replaced that with the 7 bar upper grille (fog lamp delete)... and way more airflow through the upper grille. It also eliminated the 2 x 90 bends into the oem snorkel that in turn feeds the oem airbox. Boost is 5.8 psi with oem upper grille. Increased to 6.3 psi with the 7 bar grille. ( the 05-09 cars can use the optional 9 bar upper grille).
The 05-09 Roush cars got the puny Heat exchanger. The 2010 Roush M90 cars got the bigger 18" tall x 21" wide HE.. ( which is also used on the 10+ Roush TVS-2300 cars). The taller HE gets hit by air from both upper + lower grille. Plenty of better HE's are available for the 05-09 cars
Instead of the smaller 2.49 pulley, I went to JBA ceramic LT's, + catted H, + a 94 tune. I ended up with a few hp less than a 2.49 setup, and more tq.
Anytime you have air coming out the top of the dash, the high speed ENG fan will be on. (regardless of whether AC is on or not, or just plane air coming out the top... and regardless of where the heat /cool knob is dialed to, and regardless of what speed the cabin fan is set to).
No doubt JDM has already advanced the timing to max ( for whatever octane you specified)....with blower on, in open loop.
About all you can do is... get more airflow in there with a 9 bar grille... use a bigger, thicker core HE, use 100% synthetic eng oil.. + FRPP oil filter..and engine catch can on driver's side. If that doesn't work, going to the oem 73mm blower pulley, retune, reduced boost for road course use, will help somewhat. LT's will restore your power back to what you had before with the 2.49 pulley. GT-500 style hood vents will dump a lot of heat, esp for your application. Another possible option is to use 100% distilled water (and redline water wetter for both the eng and the HE /IC loops). Then you can extract more heat.
I use aeroforce gauges on the SOS A pillar, plugged into OBD port to read the various parameters..on the fly. Then u know what's normal around town, cruising on the hwy..and on the road course. Then you can also see if any mods make any difference, if any, ..and by how much.