Placement of trunk lid, gaps?

Hello gang!

Yesterday I spent a good 6 hours in the garage switching boot lids on my Fabia 2 Combi as it was cheaper than replacing the old leaky scratched up rear window (in retrospect, no so much in terms of labour).

Unfortunately both the old and new lids don't line up well: the top of the lid is maybe 4 mm lower than the roof and there is about 10mm gap on the top. The lid also extends past the rear light on the right side about 3 mm - this is the biggest eyesore so far.

I'm not too keen on ripping the panels off again to redo this, but I'm wondering how close is the fitment on the trunk lid? I've no other Fabia around to verify from.

After a nights sleep, I started to suspect the reason for the ill fitment is on the holes on the frame for the hinge - the holes are slightly larger than the bolt, but with the old hard sealant on the frame they get "centered" onto the old spot, hence the illplacement even with changing the lid, hinges and numberous readjustments. A fix would be to scrape the surface clean, would you agree? Are there any other means of adjustment at this point?