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Sorry, bad news. If you search a bit, you'll see many threads re this problem. From what I recall, some early Vert owners had the top replaced under warranty, too late for me to do that. Window and top adjustments don't remedy the problem, as I understand it to be a design problem. Apparently, 2001 (or 2000?) and later tops have the upper, rear radius cut differently to avoid the interference.
I'm going to see if a convertible shop can cut and re-pipe it, although I read one guy had poor results with that.
As a temporary work around, we use the new window controller (plugs into the OBD II port) to roll down the windows prior to opening the door and to roll them up after exiting/raising the top. Easier ingress and egress also, as you can lean over the door with the windows out of the way!