Pins 13 and 14 usually measure only about .5 ohms to ground because they are across the relay’s coils, so it may seem that they are shorted to ground but they are not actually. I’m pretty sure that is what you are discovering here.
Because pin 6 is programmed to low when the LED is not on, it should measure a very low resistance to ground. As with the other pins, it may seem like it’s shorted to ground but it’s probably not.
First answer this: Are you sure that neither side of the LED is making connection to the parts of the circuit it is supposed to connect to? Is either pin of the LED connected to R11 or pin 6 of the IC? You mentioned this in your first post, but it seems unlikely that both pins aren’t connected to anything unless your board has been damaged somehow.
I’m curious about the socket…sometimes they don’t make good connection to the IC pins. (1) What is the resistance between the the solder joint of pin 6 on the socket and pin 6 of the IC? (2) Also, does the 4V on the IC pin change when you press the bypass switch? (3) Does the voltage on the pin change with the LED out of the circuit? I’m wondering if the LED has been damaged and is only dropping 1 volt, instead of the 2 volts it needs to light up.
Please answer these 3 questions directly.
As far as your pedal not working anymore, it sounds like there may be some opens or shorts on your board somewhere. It would be helpful to me if I could see your board. If you could send me some detailed, in focus photos of both sides of your board, that would give me a better understanding of what might be wrong.
-Brach