I'm still kind of fumbling in the dark over this, though. I've got 99 problems and organization is one.
In terms of organization, think of a tech
tree, instead of a web. Easier to map out research that way. Think of what we'll start with, then work out how each major item can be researched and upgraded. It's even possible to give Necross his organic/genetic tech, just make it so it's on par with everyone else's technological starting position.
Examples:
Starting Ship Tech: Fusion Reactor, Coilgun, Ballistic Missiles, Basic Armour (Titanium), Torpedoes.
Upgrades: Advanced Fusion Reactor (reduced travelling time), Heavy Coilgun, Railgun, Advanced BM (increased range, damage, etc.), Basic Lasers (point defence), Pulse Cannon (ballistic/energy), Heavy Armour (Titanium+), Advanced Torpedoes (increased range, damage, tracking etc.)
There could also be overlap, such as the Pulse Cannon, which would be overlapped with kinetic and energy weapon research.
Now you don't want it to be too complicated, try to keep each tree as unique as possible, like keeping the ship tech research strictly to ships. Some overlap between trees is possible, even likely, but you want to keep that to a minimum for simplicity.