You might actually be better off starting with a Borg interior and Klinking it yp as opposed to the other way around. Klingon interiors (a lot of them anyway) are especially bad for pathfinding anyhow.
Take a borg interior and use the Klingon wall lights and platforms as needed. Klink consoles and generators will also go a long way to getting what you want. The Borg mapos are pretty open in general.
Making a Borg map look like a partially-assimilated Klingon map sounds hard. But I guess it's possible. I'll give it a try.
And thanks to the "disappearing NPCs" bug, pathing isn't really my top priority right now.