Interchangeable

The augment isn't necessary, just there to have more revives overall and so you won't have to worry about refilling immediately when undying.
Primed mods obviously, especially [Sure Footed]. In place I would probably put [Cunning Drift] or [Rush].
Nourish has no effect here, just for comfort. Either way, his default 3 is pretty overkill for where we're going.
Arcanes-- do not change them. [Guardian] can be replaced, just put Molt Augmented or Molt Reconstruct for extra power or healing, even if it's unnecessary. But hey, I can't stop you.

Shards

Give the fungus boy all of your blue health and armor shards.
Make space for a yellow cast speed or two, you really want that yummy mushroom.

QoL

Not much to say here.
Just keep your stacks up to stay alive.
If your weapon is too slow for you, use Molt Augmented to make your fungus rows beefier or just put [Reinforced Bond] on your pet. Better yet, use a faster weapon.
Anyway, probably keep your 4 up as well. Anything I should say is probably just basic tips for Nidus, like the 2-1 combo.
This works pretty well in Steel Path, but anywhere else is either unnecessary or doesn't work due to his slowish-burn way of staying alive.
This fungus boy doesn't like short trips to the store, we'll say.