If the crew replaced the drives with black market units and didn't document it, then the TL9 spares the crew bring with them won't work. I am considering allowing a huge amount of jury-rigging if they make sufficiently good rolls.

Alternatively ...
Go ahead and let the PCs get the ship (barely...) spaceworthy, but stuck at J1. So long as the
Suleiman-class Scout/Courier fuel tanks remain intact and capable of holding 40 tons of fuel, the PCs could potentially do some J1+1+1 navigating across 3 parsecs from Bowman/District 268 to Flammarion/Sword Worlds.
Walston
Bowman
567-908
Asteltine
Flammarion
If you wanted to be REALLY conniving as a Referee

... you'd tell your PC Engineer, straight up, once they get to inspect the "damage" to the ship, that it looks like the drives have been ... modified ...
If the PCs bite and want to know more, you can dole out (drip by drip) that "there are a lot of non-standard parts" installed in the ship, which with enough investigation (and good skill rolls, naturally) someone might eventually figure out, "hey, I think this is illegal gear..."
If the PCs manage to get the ship back to the scout waystation at Flammarion, the line techs are going to figure out REALLY FAST that the ship is loaded with illegal modifications ... at which point it becomes important whether or not the PCs
reported those illegal mods or otherwise tried to keep quiet about it (in the hopes that no one would notice).
Depending on how the PCs deal with the "illegal mods" on the ship they needed to recover from Walston, they might get a follow up mission to track down where the black market stuff came from (and who might have sold it) ...
In other words, you could potentially use the salvage/recovery operation of moving the Type-S from Walston to Flammarion as the prelude/setup for a bigger(?) follow up for breaking open a smuggling ring (or equivalent) ... depending on how the PCs play the cards they're dealt ...
Those illegal mods open up opportunities for counter-intel/police action style campaign work for the PCs.
