hehehe, yeah, I know I'm crazy, and I might have finally screwed myself... more on that later...
I wonder why your Borg pirates didn't work?? I had no problem with them. I just readjusted the Gameplay.constants file and swapped out Pirate ships with Borg ships, added a Scout Cube and it ran fine. The only other thing I did was add the Scout Cube to the Galazy.Scenario.def file so I could plunk a few here and there with Galaxy Forge... maybe that made a difference? Maybe the only ships Pirates can use for raiding parties have to be defined in the Galaxy.Scenario.def file first???
I ran a game about 2 1/2 hours yesterday (until I took down the Pirate base itself) with no problems. All the raiding parties that hit me had Borg ships like they were supposed to. I can send you a copy of my Gameplay.constants file if you want to swap them out and give it a shot.
I also ramped up my planetary militias. They seemed awful weak, so now instead of 2 or 3 ships, my militias have 20-30, plus lots of structures: labs, frigate factories, gauss platforms, etc... so it looks more realistic. I also changed it so the militias own the planets, so you have to bomb them before you can colonize them. To me this makes militia's much more realistic.... and it gives you more things to shoot at...hehehe.
I also found out, quite by accident, that if you give the militias or pirates a trade port, and you have more than 1 pirate base, or 2 of the same faction near each other, and your in between them, they WILL send out trading vessels thru your system. Had me very confused at first because I had the trade vessel icons turned off, so I didn't know what my ships were attacking at first... they just seemed to be running around my home system shooting at nothing. But then when I turned on the trade ship icon I realized pirate and militia trader ships were all over the place.
The last thing I did was to buff up the Borg themselves... 
I know you guys are working to speed them up, I understand and I can't wait for the next release. This is just my "band-aid" fix until then. I didn't change the ship parameters in any way, I just decreased the amount needed to research the Scout Cube and Standard Cube. I left the Assimilator and TAC Cube alone. But now my Standard Cube cost 50% of a TAC cube to research, and the Scout Cube is 25% of a TAC cube. This seemed to make a huge difference, because now I'm seeing Standard Cubes after only 2 hours of gameplay. To offset this I reset the Borg to a max of only 10 CAP ships, while I still can have 16. I was a little worried about this, but so far no dumps...
So now that you know what I've done to my copy, here's my Kobayashi Maru...
I wrote already I've imported the "Sol" system planets from Distant Stars (originally the Celestial Bodies planets) into my copy. In CB and DS Gas Giants can be colonized, so I also adjusted Jupiter, Saturn, Neptune & Uranus to be colonizable with either Volcanic or Ice planet research (instead of screwing with a new research catagory)
Well, I set up a galaxy forge game of the solar system using all of the CB worlds, 48 planets & moons, plus asteroids and belts total. Player 1 (me) is based on Earth, Player 2 (the Borg) on Eris (beyond Pluto in the Kyper Belt). I also tried something new... Because the Borg AI always seems to outspend itself I set them to unfair Economist, hoping they'll pay more attention to infrastructure so they can afford to build ships. This turned out to work better than I had thought, and you all might want to try it.
The story line is you've been recalled to Earth, Intelligance believes the Orion Syndicate has been assimilated, and all contact with the outer planets has been lost.
Now I had to play this a couple times and then readjust the map to get it balanced, but on the 3rd attempt (of course) I got what I wanted... I played about 2 1/2 hours or so with no sign of the Borg, only militia and pirates, working my way out from Earth thru the asteroid belt and finally to Jupiter and it's 4 moons (Io, Eurpoa, Callisto & Ganymede). I played fast but careful, building each planets defences before moving onto the next. I also payed close attention to my Economy and research. Now playing as the Federation I've found the biggest asset is Culture, and I love the Section 31 ability (I think that's the one) where you can view any planet that's under your cultures influence, even enemy ones.
So when I jumped into Jupiter I found the Militia was chasing a couple Borg scouts... woohoo!!! I quickly dispatched them all, colonized Jupiter and began to build it up, especially 2 star bases (my gas giant planets are set to allow 2 star bases). I also sent out a couple Cap ships and escort to secure the 4 moons. But as I built up Jupiters defenses a couple more Borg scouts showed up. I took them out no problem, but then my culture line hit Saturn... and it had been assimilated...
I was looking at a bunch of diamonds, spheres, a Scout Cube and 2 standard Cubes... if there's a queen Diamond I didn't see it. And worse of all there are 2 fully upgraded unicomplexes!!!! I had to pause the game I was so stunned... For the 1st time I'm seeing the Borg as I invisioned them, and now I have no clue how to take them down!!! I have Jupiter as heaviy defended as possible; there's not one tactical slot left open... I've held off 2 big invasion fleets so far, including Cubes, and counter attacked both times to try and take down one or the other Unicomplex, but so far no luck...
So here I am in my own Kobayashi Maru... what to do?? What to do???