Looking at this more carefully, isn't it just a slug advanced to Colossal and given extra attacks? I'd think we could handle that just by changing the advancement.
The wording is rather confusing, but it does call it "an extra life-cycle stage" and its AC and move are better than the normal Slug.
The basic Megalium is "elephant sized", which suggests Huge. They should be able to advance to Colossal size "about 100 feet in diameter" for eating ships.
I'll agree to the reduced speed for the normal silver slimes.
Hmm, I'd thought the Huge description was just a part of the megalium dealing with the PCs. But I guess you're right.
And I'll agree to the many "tool attacks." You don't mean all those types of damage at once, though, do you? Am I understanding correctly that you want to give it a special ability that the tool attack can use any of those types of damage for each attack (maybe with a short delay to change each tool damage type)?
You could edit the CC entry now or just wait until the megailum is ready to go.
I'm not sure the pseudopod tools should be a touch attack, either. But I'd be happy to have a special attack entry like
Tool Attacks (Ex): A megalium can form its pseudopodia into various tool-weapons. Each pseudopod takes one of the following attack forms: hammer (bludgeoning damage, melee), screwdriver (piercing, melee), saw (slashing, melee), blowtorch (fire, ray), cleaning spray (acid, ray), harmonic drill (sonic, ray), arc welder (electrical, ray). The ray attacks are ranged touch attacks with a range of X ft (no range increment).
Of course, the Str for the slug is much higher than the Dex, so it's highly incentivized to use the melee attacks at the moment....
So they should all be ranged? I'd kind of like some difference between the normal and energy attacks.