By the looks of it, you want your code to run when the timer runs out. Calling “$Timer.stop()” won’t achieve this. You’ll want to connect the “.timeout()” property of the timer to the script using a signal and put your code in the function it creates.
Also, _physics_process gets called 60 times per second. Do you really want to be starting a timer 60 times per second? Perhaps you meant to start the timer in a different place, like _ready().