check that the clutch pedal sensors are connected. how does the engine feel? sluggish? my first guess is installation error for the flywheel - inattention to orientation of the crank angle identifier cutouts.
there is also a shaft speed sensor on the rear end of the gearbox. this tells the ecu the output shaft speed (tailshaft). in the fsm it's called input speed sensor but it's the same sensor. make sure it's connected and not damaged.
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