Window not lining up after motor replacement

Hi, wondering if anyone can shed any light on this for me?



I recently replaced the electric window motor on the driver side window on my 03 TF. All works beautifully but once I put the hard top on for the winter I noticed it wasn't meeting the seals properly and was letting in loads of water.



It almost looks as if it is going up too far, and is actually outside of the seal on the roof where the passenger one sits itself nicely central (a little bit of seal on each side).



I looked at the stop, turned it round as per some of the threads and still no joy. It actually seems to go even further up now than it did before and almost seems to skim against the hard top which is worrying - when driving you can sometimes hear it knock a little as I go over bumps.



I'm quite handy with the car myself and would like to sort it at home, so any advice anyone can give would be really appreciated.



Thanks!

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