Looking at the PCB, it seems to me that the LED could be located right underneath the pot, but the drill template has it all the way to the bottom, close to the footswitch? Can we haz a different template plz?
With a good straightedge and measurements check, I’m sure you’re gonna nail it place the pcb with the pot over the enclosure, it will give you a good starting point of the range where you can put the led hole.