Best to ask the SoA Mod team for permission to mod their mod.  Not sure what you want to do is possible or if you'd be able to sufficiently incorporate the illusion self ability into the assimilation beam.  7DS has a module that captures enemy ships, which will change the team color, if it is enabled, so best play the Borg as green color or you'll have -for one, strange colored borg and any captured ship sharing that same color.  No, you can't use our ability, we're still in Beta.

well...  if you have a tier 0 research item called, "Assimilation" for example that really does nothing but unlock an upgrade mesh in the ship entity file, then you're good.

Practice on 1 capitalship, copy the mesh, give it a Borgified texture, rename it with _Borg just before .mesh, then in the entity file give it the _Borg.mesh name and the "Assimilation" research item as a prerequisite.  Capture ship and see if the mesh changes to the "upgraded" Borg one.  Maybe you can come up with some easy Borg overlays, then apply the overlay to the dds texture in photoshop and save it.

Good luck, keep us posted.