Mission 2: Target the patrol craft first. These are fast ships that will certainly destroy you if you don't destroy them first.

Mission 3: Quickly take down the factory's shields since the gunboats will arrive soon. Make sure you destroy the frigate and transports quickly.

Mission 4: Destroy the b-wings as fast as you can since they will do the most damage. Ignore the cruiser since you can't destroy it due to its new shield. Destroy the T/As making runs on the shuttles that are halfway out of the hangar.