Put the engine back in to test that the brake and clutch master cylinders still fit. It is a tight fit around the brake (1mm) but should be enough clearance. Not in these pictures.
I couldn't help myself just had to sit in it and make engine noises. Some one has to ensure that everything is a good fit and it will be comfortable to drive. :-)
I need work out the design of the air box and where to run the clutch line. I am thinking under the gearbox.