Many thanks for all the replies. Black box was a 6v battery that is now out of the car. I'm guessing part of an old alarm system or IED. Didn't blow up yet anyways.
It had a yellow and black wire that run towards the front of the car and looks a lot like the cruise control clutch switch wires which is just bizarre. I'll get some more work done on it this weekend and let you know what I find. As for the engine (swap, etc) that's a good point and I haven't checked to be honest! I'm going to do the 1 and 7 relay bypasses to see if cranks. Also bypassing the clutch switch.
Thanks for the post about the trunk light, I'll double check that!
I also have the service manual so I'll eventually figure it out and then do a data dump of all I've leaned about whole ignition system (DME, immobilizer, clutch switch, rfid pill, programming, etc.).