You could have used several things to replace that foam piece, tape or paper folded over, styrafoam, just about anything that had a little bit of give to it and was around the same size.
The PS2 Daughter board is really nothing like the PS3 one, so you'll need to get one for a PS3 controller. Any PS3 controller from the MSU_V3.5X 1.12 on up use that type now.
http://forums.xbox-scene.com/index.php?showtopic=648322Are you just trying to get it back together here? or trying to make something else? If you're making something else you'll need to install the Pull Up Resistors on the board or it's not going to work hard wired, since they're built into the Daughter board.
Since you have solder all over the board contacts now putting it back together as a stock PS3 controller, even with all of the correct parts, isn't going to get you a very reliable controller as there will eventually be issues there.