i had an old roof with the alpine wondows in, removed the glass and cut out the 'hole' and surrounding ally. i bought a newer smooth roof and used the old roof 'holes' as a template, measured the distence from the back of the roof and marked the position of the hole to be cut.
i cut it smaller than it should have been then filed it to the correct size then fitted the glass.
easy to do if you take the time to get it positioned right and take your time cutting out.
i used an air nibbler to get it near the right size then a file to get it perfect.
ohh i am getin a new roof cos mines the old 1 with ridges down the centre just no some1 sellin a plane roof no windows i have tryed flebay but not much goin on there at the mo