I have just replaced the clutch in my 1995 R33 and cannot get gearbox to clear car body to line up shaft. There is simply not enough clearance between box and tunnel. The gearbox came out quite easy so it must go back in - somehow. I used a clutch alignment tool so that is not the issue, I can't even get the shaft inside the pressure plate at all. Any tips?

Put a jack with a piece of wood on it under the front of your engine, about the front of the oil pan and jack it up a bit. That makes the back of the engine go down at a slight angle so you can get the tranny up in there. Hope that works out for ya.