Looking back at the original text, I think we've got quite an abundance of mutations already (it seems there should be 20% with planar travel and only 1% for everything else), so I think we don't need mutations that stack at all (ie, there shouldn't be multiple mutations and certainly not 3 of them at a time). So I'll propose (with rejiggering probabilities and adjusting numbers to match caveling/troll mutate better):
1-5 - Mass Plane Travel - functions like a 1/week plane shift, except the kobalt can shift itself and up to 40 other kobalts between two Prime Material planes. Caster level X. The kobalt gains a +4 racial bonus on Charisma and a +4 racial bonus on Diplomacy checks against other kobalts. Its LA increases by 1.
6 - Carapace - Increase natural armour by +2
7 - Vomit Acid - 1/day. 20 ft. line of acid doing 2d4 damage, Con-based Reflex save for half.
8 - Extra Arm - Gives an additional off-hand attack.
9 - Claws - Each hand can do 1d3 claw damage.
10 - Long Legs - Increase base land speed by 5 feet.
11 - Whiplike Tail - Secondary tail slap attack for 1d6 damage with 1.5 times Strength bonus.
12 - Redundant Organs - The kobalt's extra organs grantslight fortification (25% chance to negate critical hit).
13 - Acid Blood - Deals 1d4 points of damage to any creature attacking it with a slashing or piercing weapon who fails to succeed at a Reflex save. The save DC equals 10 plus the kobalt's Con bonus.
14 - Strong - +2 racial bonus to Str.
15 - Agile - +2 racial bonus to Dex.
16 - Tough - +2 racial bonus to Con.
17 - Smart - +2 racial bonus to Int.
18 - Zen - +2 racial bonus to Wis.
19 - Strong Willed - +2 racial bonus to Cha.
20 - ??
21-100 - No mutation
I'm not sure planar travel requires the +4 to Cha, though the bonus on Diplomacy is good. What if we just made it a +4 circumstance bonus to all Cha-based checks against other kobalts?
I'm also not sure I like the plain ability score bonuses. They're boring.