Are there any maps on where this happened? Unless they were on a very winding road or MA had magical zig-zag bullets, the bullet would have gone through the rear window. A bullet hole to GZ driver's side window would imply that GZ was driving towards MA with their driver's side windows across from each other.
From what it sounds like their stories may not contradict one another except on the gun-waiving part:
http://www.cnn.com/2015/05/12/us/florida-george-zimmerman-shooting/
As I understand it GZ says he was followed by someone flashing lights and honking his horn and he went into a U-turn and was followed and it was in the process of the U-turn that he was shot at, which could conceivably explain GZ saying he was trying to get away while being in a position that put his driver's side across from MA's driver's side. While MA on the other hand basically says he was legally justified in what he did. It's possible that MA was acting like Audie Murphy's character from No Name On A Bullet, but I'd really want to know about GZ's alleged doctor's appointment as well as see the exact area this is with the U-turn and it's relationship to where GZ had the alleged appointment and where MA worked.