SW3 - skill tree and help needed

[Raga]

Hello,

I have just recently purchased the game on Steam.
I finished SW2 some time ago so I chose hard difficulty.
Unfortunatelly the game is unplayable for me, most of plot related enounters are too hard. One of my fighters usually is blown to pieces (in first couple of seconds) with concentrated fire of enemy, or Mothership is blown in 2-3 approaches of enemy squadron.
Credit rewards for missions are such low that I cannot afford 3rd generation ships.

I gave up having:
Astarte - 2nd System Firmware, 600 shields, Hawk scanner , 20 anti missile defense
Pilots: Hero, Trinnie (?), Greyhair
Hangar: 3x Raptor, 2x Cleaner

The plot is around finishing Alex's convoy and investigation missing convoy at place suggested by Greyhair.

Any advice what am I doing wrong?

Edit: I would like to add that I really tried to deal with it. But some missions (ie. when you are escorting Alex, one sector after saving "yellow" transport trom pirates who joins your convoy) are sick, especially when a group pf hammerheads target your mothership or a transporter. There is no other way than loading previous quicksave and hoping that you will finish previous pirates earlier and intercept missile fighters.
Please, ignore what I said above the "Edit". It appears that hard difficulty is not for me - using mechanics to maximum and playing the most efficient way possible. Medium difficuplty will be more fun for me. Just focus on my questions below.

Second question:
I started a new game (medium difficulty) with system specialist.
I undestand that the perks do not stack, but how does exactly work perks leading to Technomage? The description ststes that the bonuses work tor entire team, but I heven't noticed andy differences when putting Hero and another pilot into squadron.
Does Repairman stack with System Expert or the higher value is chosen?

Clarification: How does repairing modules work? One states the it repairs 2Hp/s but the real value is around 16hp/s when mounted on Mastiff (is it 2Hp or 2% Hp?)

Raga