Can't help on #1 as my 02 GT doesn't seem to have that connector or harness part. I'd guess it could be for an IAT sensor but your 03 (?) shouldn't have a separate IAT sensor.
#2 is the Schrader port on the fuel rail and is where fuel pressure measurements are made either for diagnosis or when installing a FP gauge. It can be covered with a standard screw-on Schrader cap (e.g. your tire valves) to keep the gunk out.
I got 02 mustang gt so #2 is your fuel pressure release thing. If you have fuel pressure gauge then you can connect there. #1 goes to a/c line next to radiator fan. Found your problem , just follow my attached thumbnail directions.