I don't see a stop button on your program. Are you actually talking about the Abort button on the toolbar?
You have some architecture problems with your VI. Why do you have 4 different parallel while loops each with its own event structure? Two of those while loops are infinite because you have a false constant wired to the stop terminal. Because of that, you are forced to use the Abort button to abort the program. That button is meant for debugging purposes, to stop a runaway program in its tracks. It is NOT meant for stopping a program under normal circumstances.
You need to redo your VI. I don't know what you are trying to do, but you might need a state machine architecture. You can probably do everything with a single loop and single event structure. You have some Rube Goldberg pieces of code in there. Wiring a Boolean to the Select function that has a True constant on the True side and a False constant on the False side makes no sense. Eliminate all of that and just wire the boolean wire on through.
