Success, I've ruthlessly gone through all my textures with this new limit:
No textures above 256x256 for Diffuse Maps
No Textures above 128x128 for Specular and Normal Maps
So far I've optimized only the Necribus Faction and now they both work together in one game!
I'll be doing the Hyperion some time tomorrow and hopefully I'll be able to have a stable version of my mod out!
So the conclusion for this topic is to be careful of memory use in both mesh frames and textures. Skeletal animation will help but with the texture limit I can see having 4/5 factions being a problem again, but for now, things are working once again!