Track IR is working really well for me in X3:AP. No tweaking needed.
I am using TrackIR 5 and the Track Clip Pro thingie that attaches to the side of a headset.
What's cool is that with the mouse cursor centered, I have the ability to shoot in the direction of wherever I am looking (within limits of the axis capability of the weapons). This makes off angle attacks and tracking moving targets much easier.
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Mobo ASUS MAXIMUS IV EXTREME (REV 3.0)
Memory CORSAIR XMS3 8GB DDR3
GPU 2 MSI R6970 Lightning Radeon HD 6970 2GB
CPU Intel Core i7-2600K Sandy Bridge 3.4GHz (3.8GHz)
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UPS Cyberpower PP2200SW
PSU Antec High Current Pro HCP-1200 1200W
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Drive LITE-ON Black 12X Blu-ray
CPU cooler Noctua 6 Dual Heatpipe
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OS Windows 7 Premium