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:
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It’s a little hard to see but it was there. Easy enough to adjust if you haven’t before. Simply pull the weatherstrip away from the channel to reveal three screws:
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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!
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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 it’s 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.