The heat signature of the engine, which in part is connected to the entire plane. Burning that much jet fuel produces a tremendous amount of energy. You literally have a glowing ball of energy streaking thru a vast void of no to low energy. Clouds have heat, but not at the huge concentration a fighter jet has.
I guess you have flares, but now its an "AI" problem of choosing the right target.
I'm no expert at this but I think the efficacy of infrared detection would depend entirely on the elevation of the plane and its size in arc seconds. What's the resolution of your detector? Is the time it takes for the plane to move from one pixel to the next shorter than the time it takes for photons to gather on the sensor above threshold?
Don't forget the inverse square law of light, by the time the energy reaches a detector on the ground, the signal has weakened considerably.
Skimming wikipedia for infrared stealth gives me "Infrared Search and Track" systems which are plane-mounted, which makes a bit more sense to me -- if you're closer to the targets altitude and velocity you'll get much cleaner data
I guess you have flares, but now its an "AI" problem of choosing the right target.