There was the problem of moving the pipes down to fill the empty voids you created when removing the connected pipes. The problem is my entire map is draw based on an array of tiles in layers. I came up with an evil genius way to get around that. I made an array of floats that will be used to offset the pipes from their "real" location, and once they move past one tile in pixels I teleport their tile location and set the offset back to 0. There is some overdraw as the tiles move, but they move so quickly you can barley notice it.
I made my first pipe mania video preview if anyone wants to look at a REAL puzzle game :D. The career mode is the match 3 prototype thats going to be used for the real gameplay. Of course I am only doing a flood fill only when I rotate a pipe, so thats why you can see alot of connected pipes that are magically staying on the map.