I ended up taking a drive with the top up. I can recommend doing this occasionally so you can find problems you might not otherwise. Interior seems quieter now, however I did notice some wind noise coming from the passenger side at the back of the window. Got home and had a look, there was a bit of a gap between the window and the weatherstrip:
Its a little hard to see but it was there. Easy enough to adjust if you havent before. Simply pull the weatherstrip away from the channel to reveal three screws:
They are in oval holes to provide for adjustment. I loosened all and pulled the bottom as far as I could towards the outside, then tightened the screws. Replace the weatherstrip back in the channel and voila!
Had her out again today top up and that noise is gone. The shifter is making a rattling noise now, it goes away if I lightly touch it. I figure its either something not assembled correctly after my transmission fluid change, or maybe the new shift knob is a different weight. Either is easy enough to test.
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