There are 6 items of equipment with unique means of acquisition. Four are available through dropped loot and the others are available through finding unique lockboxes. Much of the information gather together on this wiki stems from Tamina's forum thread.
High-end equipment for the Skunk available through crafting items dropped as loot:
High-end shields for the Skunk are available through crafting rare items (details here):
Spami provided information on all crafting recipes. After all required items are collected, crafting can be undertaken at any time. This is achieved via the Inventory menu (Return-2-1-3 through sidebar, or <shift>-I).
in order to fit most of these items, a special mission must be found and accepted (SETA does not have an associated mission). Once the item is crafted for the mission, it must be returned to the respective NPC (so don't accept these mission offers from soon-to-be hostile stations!) in order to fit it, at which point you can sell the item or ask for the equipment and you'd be directed to an NPC Mechanic who can fit it.
The Mk5 Engine & PR3 weapon requirement can be crafted & sold repeatedly without needing to find the relevant mission, but you'll lose some extra cash. The mission is only necessary to fit the equipment to the Skunk (or create & fit in the case of the PR3). SETA can be crafted repeatedly but its resale value is less than it's individual components, so not worth the bother