So today I massively gutted the game to make it conform to MCV standards. It meant breaking up my FlxSprites because they contain all the model data also. I also did a ton of optimization and the new code is smaller and streamlined and much easier to write and modify. Unfortunately I just started putting the view together, so my end result is less than what I finished with yesterday.
I also changed the way that levels are loaded into the game. The old way was extremely manual and the new way can be completely done from in Tiled and is much faster.
I guess the moral of the story is sometimes you have to go backwards before you can go forwards.