Ummm, R33 Skylines DO NOT use a distributor system, they use an igniter and direct-fire coils.
Here are a few minor things to check:
are you sure it's nothing to do with your alarm and/or immobiliser shorting out somewhere or playing up, and therefore cutting off your spark and/or fuel?
when the engine is COLD, remove the radiator lid, start the car (if it will start), and see if there are any bubbles appearing in the radiator fluid. This could indicate a blown head gasket...
when the engine is OFF, remove your oil filler cap, and see if the oil looks dark and "clean," or if it's a cream-cloured sludge. Do you know if it was blowing a bluish-grey smoke out of the exhaust at all? This is another sign of a blown head gasket, as the oil and water are mixing and creating that sludge.
HOWEVER, considering you saw a big puff of black smoke, I'd say it's either a massive dump of unburnt fuel, or your car is burning oil, which could mean a few things are wrong, including blown piston rings, or maybe even a blown piston...
I'd suggest taking it to a (different) mechanic, and getting them to investigate a bit further. I doubt it has THAT much to do with your boost controller.