Generally people do it one of two ways. Either pull the lag bolts holding the engine mount to the boat, or (and this is the one I use) undo the nut off the top of the mount and leave the engine mount in the boat. That way the bracket stays on the engine and as I have a stand I made, it fits nicely onto the posts I made. As for alignment of a new engine, don't rely on the previous engines' alignment, start fresh and get it right first time....
Chris........