Not the door opening. The actual channel itself where it's tight. That stuff is very tough, but if it's too closed up it just has to be widened a bit.
When you were adjusting the lower sections did you leave the bolts loose and run the window down? This can let the channel float into it's natural position where you can then lock it down.
I wonder if it's also a tight spot in the regulator doubling up with a new tighter channel.
Paul