I figure since the new DLC basically adds the units you had previously, the rework would focus mostly on mechanics. As a bonus if you work with units already in the game this means maximum compatibility.

1a. Slave casualties for Throt produce Growth Juice, numbers can be tinkered with but I'd suggest something like 1 juice per 10 salve deaths, improvable via buildings in the upgrade chain and potentially new research. You'd also be able to perform a new rite which kills 10% of your Slaves for a growth juice and temporary food per turn boost that's proportionate to the slaves killed (say 1 food per 5 slaves since they're being mutilated for Growth Juice extraction and the remains are what's left to eat) to trigger this mechanic manually. The Crone has a similar mechanic you could basically rip off to trigger this, with a different conclusion.

1b. Ikit could have Slaves in regions with the appropriate buildings generate Warp Stone in addition to additional upgrades which use warp stone (scrap system based because with systems like these, you need a resource dump or they just accumulate with no purpose and the workshop to my knowledge can only provide faction-wide buffs not single unit buffs)

1c. For Queek, I'd suggest saying screw the slave mechanic past the income aspect and instead give him an Empire Electorate College with other Skaven (He is a member of the 13 after all). After battle make Queek decide slaves or Trophy Heads. Slaves give economy, trophy heads give favor with the other Skaven factions which eventually will result in confederation with some convoluted lose-based narrative scenario that you can justify as the mcguffin lol. Again, it's taking the Empire's Electoral College and re-tooling it for Queek, using Trophy Heads as the main way to gain favor. I'd also suggest giving Queek's units the ability to be upgraded via the scrap system with Trophy Heads as a resource sink.

1d. Skrull can use a rite to infect 10% of his total slaves, next turn this spawns a neutral peasant mob (and/or other units) army that is proportionate to the number of slaves sacrificed.

This army will have permanent plague and will travel immediately to the closest non-skaven/chaos/norsca/beastmen owned settlement (make sure to include these races or other race mods can mess this system up) and roll for 1 of 4 outcomes.

1st outcome is the army moves immediately onto the next city.

2nd outcome is the faction declares war and the city's garrison (and lord if there's one present) fights a battle with the neutral faction.

3rd outcome is the neutral army declares war and sieges the city.

4th outcome is the neutral army is confederated.

The other thing the neutral army will do is have a percentage to spread a plague to the city it's at per turn and a small chance to spread the plague to the region it's in per turn passively.

Outcome 1 should have a 0% chance
Passive end turn should have a low chance
Outcome 2 and 3 should have a medium chance
Outcome 4 should have a high chance

The amount of slaves in the army should influence the chance percentage for each of the above situations or outcomes.

This clan won't need a resource sink as infecting the world is kind of their theme and if you keep the ritual cooldown at 1 turn.

1e. Eshin can sell slaves with a rite for "favor"
Favor can be exchanged for Actions or Contracts in Shadowy Dealings.

If 10 Contracts are completed against a specific faction it triggers a Greater Clan Contract to kill that faction's Legendary Lord. When successful each province of that faction will become a new, neutral faction, defeating the faction target who lost the Greater Clan Contract.

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I'd also add a Skaven race-wide store for items, using trade routes with other skaven factions to lock items (or ownership of capitals if that faction is dead) and if possible a bunch of items with randomized shop inventory every turn.

Anyhow that's my idea! Easy to tear apart and make your own if you like any aspects of it!