Playing through Star Wars: X-Wing vs. TIE Fighter finally gets moving again with Rebel campaign mission #14.
After several weeks of beating my head against this on Medium difficulty, I finally gave in and switched to Easy. What a difference! Easy difficulty reduces the number of ships you have to inspect, making the mission reasonably playable.
I'm not saying Medium is impossible, but it's close. Trying to get all the ships inspected and disabled before they start getting gobbled up by the SSD is extremely difficult. On Easy you at least have a chance.
The strategy on any difficulty is pretty straightforward: Inspect everything, disable the ships containing conscripts, keep the rescue shuttles from being destroyed. Targeting the freighters early to make them launch their Advanced Concussion missile will make your life a lot easier.
Your wingmen will take care of destroying freighters carrying warheads, allowing you to focus on disabling the ones carrying conscripts. On Medium difficulty, you'll have to spend a lot more time dogfighting TIE Fighters. On Easy, your wingmen are much more effective dealing with enemy fighters.
Good luck, and keep flying.