First things first... make a backup copy of ShipComponents.xml file in the ...Steam\steamapps\common\Star Control - Origins\Assets\Ships folder. [You may wish to rename this copy to ShipComponents-Original.xml or something to that effect.]

Modify the cost of module upgrades easily by adjusting 'cost=' line for any modules you wish to adjust in the ShipComponents.xml file.

***WARNING***
You can also modify other statistics for modules, but take care as adjusting these values may negatively impact game stability.