Great questions and point, Scrap! Here are some answers and an example.
Combat Commands are my top level unit. Using the Combat Manual Kurita and Merc. books (and my best guesses for the other houses using old books), I've made a force sheet for each faction.
Each combat command has a number of values that determine its ability to win battles. These are PV, Damage, Quality, Loyalty, Weight, Leadership, Equipment, Upkeep, Fatigue, and Morale.
PV represents the operational size and ability of the unit and ranges from 1 to 100. Each point roughly translates to a single 'mech. (While I know that a Combat Command = 1 regiment of 'mechs = 108 individual 'mechs or more for a reinforced regiment, for simplicity and to represent that every command is degraded during the Succession Wars, I've set the max as 100). PV affects the damage a unit can inflict on an enemy command and degrades as a unit takes damage itself. When not using the Abstract Rules (i.e. when using Alpha Strike), the GM uses these values (almost always multiplied by the type of engagement) to determine the max PV of both sides.
Damage is simply PV/10. It of course is modified by many factors as stated in the table in the first post.
There is no armor rating, but units do have ways to reduce incoming damage, as indicated in the table above.
It may be preferable to have units track both damage to armor versus 'mechs destroyed, but right now it seems like an unnecessary complication.
An example:
The Federated Suns players order the Eridani Light Horse, 21st Strikers to attack the world Dieron, currently only by the 9th Dieron Regulars, under the control of the Draconis Combine players.
Here are the current modifiers for the abstract resolution roll for each Combat Command:
Eridani Light Horse, 21st Strikers
PV 91, Quality +1, Leadership Rating +1, Loyalty +0, Weight +0, +1 for higher relative PV, +1 for Superior Doctrine
9th Dieron Regulars
PV 73, Quality +0, Leadership Rating +0, Loyalty, Weight +0, -1 for lower relative PV
2d6 + (Attacker ELH +4 to roll) - (Defender 9DR -1 to roll)
2d6 + 4 - (-1)
2d6 + 5
GM rolls a 5 (2&3 on 2d6) and adds the total modifiers from both sides (+5) for a result of a 10 and consults the appropriate row of the resolution table.
The result is a Victory for the attack with a x1.3 multiplier to attacker damage and a x0.7 multiplier to defender damage. The GM now calculates damage to both units from the battle.
ELH to 9DR: [9 (base, PV/10) +0.1 (Veteran quality) +0 (medium weight) +0.1 (Superior Doctrine) +0.1 (Assault order) +0.1 (def's Fanatical Defense) -0.1(def's Defend order)]*1.3 (attacker victory, 10, battle resolution multiplier)
ELH to 9DR: [9+9*0.1+9*0+9*0.1+9*0.1+9*0.1-9*0.1]*1.3
ELH to 9DR: 15.21
ELH to 9DR: 15
9DR to ELH: [7 (base, PV/10) +0.0 (Regular quality) +0.2 (Heavy weight) +0.1 (Fanatical Defense) +0.1 (Defend order)]*0.7 (attacker victory, 10, battle resolution multiplier)
9DR to ELH: [7+7*0+7*0.2+7*0.1]*0.7
9DR to ELH: 6.37
9DR to ELH: 6
The attacking ELH inflicts 15 damage on the defending 9DR (degrading their PV from 73 to 58), and the 9DR inflict 6 damage to the ELH (degrading their PV from 91 to 85). The defenders (9DR) will now have to make a morale check or be forced to take a retreat order for the next turn (or possibly surrender if they roll very poorly), and the attackers have a chance to recover salvage from the battlefield (and possible recover some of the damage they just took.