I've read the combat code, here's what i see...

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units are grouped by acs fleet then by type; a group is all units of one fleet of one type.

add up each group's total weapons, shield, armor. adjust attack of each group by a random modifer between 80% and 120%.

damage is pooled together for att side and def side, but it knows the pecentage that came from each unit type. damage is split up to the different groups by ship count (1 ship = 1 ship).

RF multiplies damage in proportion to the units and the RF rating. a cruiser hitting all LF would do normal damage, then normal damage*6. (ends up being x7 total, bug?). IE, when LF take damage, they check what percentage came from cruisers, that damage share is increase by the RF multiplier.

total damage dealt to each group is mitigated by the groups own total shields (not shields of other groups.) if damage gets through:
losses for a group = (unit count) * ( (group's share of damage) / (group's sum armor) * (0-200% random mod) )
EXAMPLE:
1 LF takes 80 damage. zero techs.
losses = 1 * (80 / 400 * 1.48) = 0.296 (rounds down to zero losses.)

in fights, there's a number of shots fired for each side, equal to number of units shooting, adjusted by RF.
max units lost in a group = (units_in_group) * (total_enemy_shots / total_attacking_units). ie if enemy shoots 9 times, you have 10 units, you can never lose more than 90% of any unit group. (RF seems to jack up shots fired a lot.)

lost defense units: you recover between 56% and 84%, randomly determined for each defense type.
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at beginning of every round, armor is considered healed along with shields. surviving units dont remember previous rounds

Here's a sim showing layered fodder in the defense. shields of grav and terror handle the small damage until they're the next up.

[Blocked Image: http://i.imgur.com/IusWBhM.png]