I never had the problem that your facing. (I found those missions to be easy when I played them) I actually stayed and played tag with the ties for a while.
Couple of tips:
Uncle Antan: destroy all of the ships that are originally in the area, the proceed to dock. Put full power into the shields and then shoot the new fighters as they leave the station.
Probe mission: Keep moving, first part of the mission, set lasers to zero and shields to full. Use missles to destroy the probes at first. Also use the capital ships to your advantage (Weave in and out of them). When probes are launched set lasers to +1 of normal recharge and dropped shields to +1 of their normal level
Once everything is destroyed turn shields back to normal and dump all laser power to your engines and run for the hyperbouy.
"Dulce bellum inexpertis."
Official Forum Expert on Norse Mythology
As Odin says in the Hovamal:
"Praise no day 'til evening; no wife 'til on her pyre; no sword 'til tested;
no maid 'til bedded; no ice 'til crossed;
no ale 'til drunk."