You are doing the right thing. It depends how "deep" the scratches are in the roof. Are they just micro fine scratches or deep into the clearcoat? Z5 is the way to go to try and remove any marks in the paint--several coats would be good--do the whole car though, not just that one area. You mentioned Z6--it's a GLOSS ENHANCER, not a GLASS cleaner. Spray Z6 on the car and wipe down in between your Z2 applications--makes a huge difference. Z12 is their glass cleaner--DO NOT put Z6 on your windows! Go to the Zaino site and read how to apply the products--just to make sure you do it correct. They will also send you an instruction sheet.
I have about 4 coats of Z2 (w/ZFX) on my Crossfire and it's awesome! After your first coat it will be 10x easier to apply on the second, third, etc... If you have any questions let me know (it seems comfusing to use Zaino--but it's really not, and you will be happy with the results!)
Let us know how it comes out!