Cobb does not recommend running intakes on their maps. They are testing the SPT intake but as far as I know they haven't told us anything yet. I would go back to stock while you are flashed stage 1, if you really want to use the intake you could get it protuned but I don't know if that'll really help.
for number 2, the Accessport doesn't allow you to take logs or read readings from the ECU. He most likely had a laptop and some other software to do this.