I have noticed that the driver's side door appears to be sagging.  The distances between the door plane and the hood plane, etc. seem okay, but the big black rubber/plastic molding doesn't line up.  It might be off even 1/2".  Last night I deduced that perhaps when the battery was replaced a year or so ago that the panel might have been misaligned when it was reinstalled, and that really is what has caused the car panels to not line up...  Is this a possibility?

Without photos of the door gap all the way around the door frame its hard to diagnose where the problem is.

Yesterday I dropped a tool into the recess behind the panel, necessitating removing it, and I got it aligned better -- there was enough play to make it right.  Apparently the people involved in replacing the battery didn't care enough to pay attention.  I will try to track down a TORX tool that fits the lowest leading bolt better in the future, though...