If you're doing any vinyl on the roof Alan, i'd extend your 4" idea to line up with the B posts, that way it would tie in with the tinted rear widows and look more like it's meant to be.
Either that or do the whole roof or nothing, just sort the paintwork.
Milliput is amazing stuff, i first used it errrr......... years ago during my apprenticeship. I call it "plasticine for Grown-ups" as once you've moulded it into shape, it stays there and sets hard. It's not great at "thin layer adhesive" but does stick well when used thickly. Repaired the mounting holes on my under-dash panel with it :
Before ^^^^^
After ^^^^^
First time i'd used it for years, not perfect but very close to the original shape and is still doing well.
You've alreday made vast improvements to many areas of the car, no need to panic over getting everything done and dusted quickly although it's nice to see the enthusiasm!