This is how it looked when I first bought it from Bob Wise, he of Miss D'Meanour fame, for those that remember it. As you can see there was not much to it, just a body with a borrowed chassis to line it all up. 
The following pictures tell how I, and friend Mick, chopped the roof.
On the right is the body before the roof chop, and below, after. I wanted it chopped so it looked "right" but not slammed, so I chopped it 2,1/2"at the back and 2,1/4"at the front.
Roof finished, the following photos show how we got to this stage.
 Mick makes the first cut, gulp!
Roof off, no going back now!!
 The welded centre section, in hindsight the front cut should have been much nearer the front screen. This would have made it much easier to line up the roof section, and also use the original seam as used by Ford. (we did not know it was there till after ~ grrrr....)

Welded rear quarter, with essential "dogleg" cut by rear window.
 The roof back on & welded.
Mk III Cortina roof panel fitted & fully welded in.
Inner wings & floorpan-(where?) not much left of the original left!