Yeah, unless running out of fuel (coal, Accumulators, Dilithium Crystals, whatever) is a common occurance, just roll it under Prudence.
As for the Cortex, making one is part and parcel of making a Steamjack from what you've said. Roll it into the crafting check. A salvaged or ready made Cortex should be treated as raw materials, Aegis or someone more conversant with the setting could probably help there more then I could.
The jack itself is the Prize, the Cortex is just a part of it. In a different setting where, for instance, jack like constructs were biologic/alchemical in nature and dropping the Cortex into a vat of goo and waiting a few hours or days for your new mount, then I'd say the cortex is the Prize, the jack is just how it's expressed.
This is based on, from what I can tell, a Cortex isn't really useful for anything outside of controlling a jack.