I have not replaced my top yet, but I've read a bunch of threads saying how tight the top was when it was first put on the car... and how important it was for the top to be left UP when the car is not being driven.
If the top looks brand new and it's tight, I'm betting it just needs to be kept up at night for a couple of months and helped to close for a while.
Who knows about the motor noise though. I'd say enjoy the car until it breaks and don't sweat it. Life's too short to second guess something that may not happen for years.
I can't wait until I have a new top and have this same concern