Updated.
Organization: Solitary or group (1 plus 2-6 shadowsponges)?
Challenge Rating: 6?
Anything else?
I'd add a larger group:
Organization: Solitary, group (1 plus 2-6 shadowsponges) or herd (1-6 plus 5-40 shadowsponges)
How can they be called Herd Clouds if they don't have a herd?
Challenge Rating 6 seems reasonable.
Still think they need an extra Hit Dice, since the original Herd Clouds were 8+8 HD:
Herd Cloud
Huge Aberration
Hit Dice: 8d8+64 (100 hp)
Initiative: -2
Speed: Fly 30 ft. (6 squares)(average)
Armor Class: 11 (-2 Dex, -2 size, +5 natural), touch 6, flat-footed 11
Base Attack/Grapple: +6/+18
Attack: Slam +9 melee (1d4+6)
Full Attack: Slam +9 melee (1d4+6)
Space/Reach: 15 ft./10 ft.
Special Attacks: Engulf, lightning, overrun, steal air, toxic fumes
Special Qualities: All-around vision, oozelike, sense air
Saves: Fort +14, Ref +0, Will +8
Abilities: Str 18, Dex 6, Con 26, Int 11, Wis 15, Cha 7
Skills: Diplomacy +9, Search +4, Spot +17
Feats: Endurance, Iron Will, Weapon Focus (slam)
Environment: Space
Organization: Solitary, group (1 plus 2-6 shadowsponges) or herd (1-6 plus 5-40 shadowsponges)
Challenge Rating: 6
Treasure: None
Alignment: Always chaotic neutral
Advancement: 9-16 HD (Huge); 17-24 HD (Gargantuan)
Level Adjustment: —
Lightning (Su): A herd cloud can generate bolts of lightning. Twice per day it can produce two 400-foot lines of lightning, each dealing 6d6 points of electricity damage. These "twinned" lightning bolts cannot overlap. Once per day a herd cloud can produce a lightning bolt that strikes a target within 400 feet for 9d6 points of electricity damage and then forks out to hit all targets within 30 feet of the initial target for 4d6 electricity damage, in a similar fashion to a chain lightning spell. A DC 22 Reflex save halves the damage of any bolt. The save DCs are Constitution-based.