06 v6 convertible window not aligned

That window is actually going up properly I believe. It is a common problem though that the window doesn't move easily in the channel and leaves a gap because it doesn't close all the way.

You can grease the channel (lithium or other product) and the window will go up all the way and seal against the front window. Try that first before doing anything else.

Try pulling it by hand to see if it will go into place then. I had to do that on my 2006, 2013, and 2017 at times. If you can pull it into place, then I would check the channel to see if it is pinched somewhere so that the grease isn't enough.