Feel like an idiot about the black box, it was just the cover to the throttle bracket, the hoses and a few wires that sit on top of the engine, HELLLLO. With it removed all went according to recieved instructions. I think we got er beat.
Thanks to all, if I was closer I'd buy y'all a beer or whatever you may enjoy.
Did what jeffsimons suggested, lowered the air intake bracket (cut and drill) and modified the throttle bracket (cut and weld) to clear. Tapped down the vacuum on top of the engine as Mrfuelish suggested, very little. Its a tight fit and we may still need to cut the braces off the hood but if we tinker with it a bit more one might get better clearance. Only had half an hour in the shop today so we didn't get it all cleaned up, but hey the hood closes.
Jeff when you mentioned not being able to get the one bolt back in I presume it is the one right under the rubber boot. We will try and figure that one out while we tinker tomorrow.
Again thanks to all for the advice and ideas, I guess once a fella gets some ideas and advice from those in the know and then eyes up what has to be done voila. Stay tuned and await the next challenge of my Sami Su's, I'm sure there'll be more.