It doesn’t make much sense to send a ship of any kind (let alone a long range vessel) out in space without a ‘fabrication bay’ or high end machine shop in order to replicate/build/manufacture parts needed for an emergency repair. Ships aren’t going to be sent out with enough spare parts to rebuild their entire ship and every support craft and component.
The main issue with that (for Voyager and other ships that might be in a similar situation) would be fuel/energy required for the use of those shops.
If you are trying to replicate the feel of Voyager, I would suggest adding a situational trait to the game (from the session they get ‘stranded’ on) called ‘Resource Cap’ with a specific number attached. Each time the ship drops their power level by half, or has to repair their ship, or replace a shuttle, reduce the number for the resource cap. With this, you could also spend threat in a given scenario to ‘drain’ their available resources by a certain amount.
Whenever they find, acquire, or trade for resources, add a specific amount to the resource cap. This might help simulate the stranded feeling for the crew.
As for the rolls required for replacing a shuttle, no clue on that… In my campaign, I am about to have my ‘crew’ of players build a new Runabout at a Starbase. Not the same scenario, but I was going to do it as a series of extended tasks. 4 extended tasks in total, based on the following:
Structure. (2x Structure for work track; 1-2 Resistance; 3 Magnitude; 1 Interval equals 4 hours.)
Engines. (2x Engines for work track; 2-3 Resistance; 4 Magnitude; 1 Interval equals 6 hours.)
Weapons. (If any, 2x Weapons for Work Track, 2 Resistance; 3 Magnitude; 1 Interval equals 6 hours.)
Subsystems. (2x average for Sensors, Comm, and Computers for work track; 1 resistance; 3 Magnitude; 1 Interval equals 8 hours.)