Heavy use, poor maintenance:
The ship has seen its share of action and parts have been upgraded, swapped and downgraded multiple times already. Whoever was doing the work was either in a rush or didn't care about the ship because the bones of the ship, the panels, nuts and bolts, have all been heavily damaged due to wear and the careless mechanics that came before. You're looking at a lot of manual labor to repair the damage and the use of a repair bay to ensure it's done correctly.
Effect: Upgrade the difficulty of all Mechanics checks on the ship.
Cost to repair: 12,000
Difficulty to repair: Hard Mechanics (3 Difficulty)

Damaged wiring
As noted above, the lack of care when adding, modifying and removing parts has taken its toll on the ship. The wiring throughout the vessel is damaged and corroded, requiring replacement. While a relatively easy job for a skilled mechanic this is an expensive procedure requiring a lot of downtime and a place to dock.
Effect: Reduce System Strain by 2.
Cost to repair: 8,000
Difficulty to repair: Average Mechanics (2 Difficulty)