From the looks of those pics, I can say with about 80% confidence that that pipe will not hit the hood. I have a 3" pipe running over the top of the engine that sits higher than that. The only concern with the height of that specific setup is a rib on the passenger side of the hood (about 1/3 of the way from the pass side, runs diagonally).
That being said, it looks like you are using a generic ebay SS manifold. I am using the same type of manifold. I cut the turbo flange off and rewelded it at a slight angle on a horizontal plane towards the head light and rotated it away (counter clock-wise when looking at it from the front) from the engine on an axis parallel with the engine/crank/cams. I also used a T4 flange as a spacer. For reference, this is with a 62-1 Turbonetics turbo.
I have mine shooting down towards the shock tower. Ideally, it would be straight down but I had issues with the manifold runners. I was able to put a 90 degree elbow on it and shoot it back under the power steering pump. Another two angles (45 and 45 I believe) make it end up inline with the length of the car and heading straight for the intercooler.
Plumbing intercooler pipes can be a pain, but if you get them setup right the first time, it makes all the difference.