I really just don't understand the failure of the water management system. It's so fundamental to get that right. I was going to mention that the real seal along the edge looks too exposed - a minor knit when you (were) so happy to begin with. Mine was too much exposed - I had them fix it.
I like the mod on the inter-liner clips. Are the wheels exposed a little from the inside with it closed? Look up and to your left while seated.
I get a whistle up and to my left. The dealer told me its normal. It wasn't always there and not immediately after the top was replaced. I can make it come and go by switching the A/C between recycle (no noise) and no recycle (noise).
Hang in there.