Hello,
Very good point, these are not actually clearly listed anywhere other than in the code examples. I will put together this info on the Pepper wiki later in the week but in the meantime here's the quick answer.
LED output pins are as follows from left to right:
PD: 17, 18, 21, 13, 14, 11, 12, 15, 16, 19
CPP: 6, 7, 10, 2, 3, 0, 1, 4, 5, 8
Buttons input pins
PD: 26, 25, 24, 23
CPP: 15. 14. 13. 12
Trigger input pins when configured on the back (shared with the buttons)
PD: 26, 25, 24, 23
CPP: 15, 14, 13, 12
I'll put together a more comprehensive page shortly.
Yes, the inputs can be configured separately. You can choose which you want to be analog and which digital.
Hope that helps.