A few thoughts...
For a GT LPF you should be on software version 205MOD, you shouldn't really have any problems running that software on maximum timing or punch.
A 6.5 in 4wd with the LPF may be pushing the ESC's abilities a little. Not sure how that would necessarily result in the motor overheating, but it may be a reason. Is the ESC itself hot after a run?
Drag brake generates a huge amount of heat in the motor, ideally run it at zero and brake manually, 10% as a maximum setting if you can't get along with that.
Apart from that, the most likely mechanical issue is drivetrain drag. If you are not experienced with the cars it may be hard to know how free it should be so put it in some experienced hands. With the pinion off, the car should roll freely along the kitchen floor with little more than the inertia of the wheels and tyres to overcome.
I don't know the SX intimately, but as an example, my Yokomo B-MAX4 suffered from bad mouldings in the centre transmision that pressed on the bearings and made the transmission very tight. It took me a cooked motor and some thought to realise this, and a less experienced builder would probably never notice it. Another common example with some other cars is that it is possible to over-tighten the wheels and lock up the bearings.
It's possible that just one axle, shim or bearing in the drivetrain is tight and that is all it takes to overheat motors (and affect the handling too).
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