Is there some kind of lock or bar that is keeps the window from going all the way down? Can it be removed?

 

There isn't enough room for the window to go all the way down. There's nothing you can do to change that short of changing either:

a) the shape/function of the glass
b) the shape of the door

Are either of these possible? With enough money and time, I'm sure everything is possible. Plausible? That's up to you.

 

Damn, my dumb *** never thought of that.

 

Sometimes, the obvious answer is the first one overlooked. At least you asked and searched instead of taking apart your door and then asking how to put it back together later, which means you're following the old "Measure twice, cut once" kinda rule. Keep it up!