Sometimes I cut 2 pins and sometimes 4, it depends of the lengh of the pin header, and not all the plastic rings of the audio jacks are needed.
what about the polarity of the led? Does it matter in this case and yes how do i align it? It has a long and a short leg: does the long or the short leg come on the side marked with D5?
It matters, in the silk screen you can see the flat side (next to the D5 text) this is the cathode.
This short lead (cathode) goes to the flat side of the diode, like the image below:
You say the jumper on JP1 is optional. What function can it have when soldered?
The jumper 1 basically moves the virtual ground from 1.6V to 0V when it is placed. Doing so, the ADC0 will digitalize the positive part of the guitar signal and the ADC1 will read the negative part of the input signal. Similar to the "
Double Span and Digitize Signals Using Two ADCs" (check Fig.2) It works but it is kind of experimental feature, I will prepare a topic to explain how it works in detail.