That black box is a fusebox, the 12vdc comes from the battery switch, red and black wire. It feeds that box, and passes through to feed the digital switchbox (box with two studs on it up under the steering column)
Check the ignition switch for power in the start position when cranking, running, check the digital switchbox power (studs) as well. That will rule out a problem with that black box, I think. Check the kill switch connections as well, and the kill switch on the SHIFTER. Have you checked that one?
If that doesn't fix it.......it sounds like a timing issue, mixed up plug wires (is that even possible on this engine?) cam timing, possible damaged valvetrain, something like that. SO the very next thing I would do would be a compression/leakdown test on the engine.