Attach smaller islands to the main fortress. The small islands will be weapons platforms and docks for flying creatures. In fact, shape it like a chaos star. Each spike is another island coming off the main body.
No. Shape it as two concentric circles.
Diversity doesn't mean a bunch of medium strength. It means some medium, some heavy, some light. For this? I'd say we need light weapons for close range defense, and heavy artillery for long range support. I love inventing stuff. So...for our point defense? Those tortoises would be very effective against boarders,even if they are tiny. But being tortoises, we need a fast reaction force to keep them from getting too far before they arrive. Thus, I suggest Chargers. Modified big cats, to be longer, with an extra set of legs, bigger teeth, and stronger body. No wider, ally, but basically, make them built for speed, with thick frontal bones to let them smash into enemies, and then tear into them. The pouncing is the part we like. Against flyers, we need a versatile weapon system turret. A tree, made to be flexible and bendable, of it's own accord at a low skill level, or it could be targeted manually by a more intelligent and more capable Stem(basically connected their growy hands to it) needed. Thus; no need for constant manning, and no unneeded resources spent on making it fully automated when not necessary. These could grow on them the following weapons:
Flack Pods, semi-aware seed pods that explode into shrapnel when they are near an enemy; it's bloody hard to hit those fast ones directly.
Flair Seeds, small(relatively, maybe two inches diameter) seeds that have a chemical reaction ncreasing their temperate incredibly en route, and thus grow in effectiveness the farther away the enemy is, to a point. Still effective up close, what with the high speed sharpness.
Fun Spores, spoke pods that explode into drifting spore clouds, dispersed easily and carried away by the wind...such as that in the wake of the enemy flyers.
For heavy artillery, similar, but really just giant mutation things(probably look like a combination of fungus and animal, to get the needed force), to launch various Shells. Especially Fire and Vine ones. Fire has no real shockwave, unlike solid, but starts a hearty conflagration! Vine ones have semi-sentient vines with thorns and the like, which ensnare and strangle their victims. Acid shells would be helpful against armored enemy formations, and air burst ones could spread fungi spores or poison, especially with Krait's help. His power, I feel, would be most beneficial in just making it so all our projectiles are guided, essentially. Woo winds!
Breeding chambers are a must, I have to say. And so are heavy transports to get our big guns across the field. Speaking of which, we need big guns. I say we merge an elephant with fungus, to make a mobile artillery piece. and we still haven't made our stems grow their own weapons, or made any new dreadnought. We could probably make them rather cheaply simply by using just life. Wooden core with bone plating, covered by a chitin shell to protect it from heat or slashing? And then the various things it. Could grow on it? We have our Life Guard.