I would design the program differently.

You also have no monitoring of whether a limit switch is exited.
And there is also no monitoring of whether the cylinder travels the respective path within a permissible time.

I downloaded your program and start the simulation.

Your last setting is that both limit switches are active and i can start the program.
Did you mean that is correct?

The next is:
I do nothing chance by the limit switches and the program change the ouputs every cycle.
Did you mean that is correct?

Try this.

You must chance the timer values and the number of loops to your wish.