Not going to want to hear it but the pipe extentions, proper rain cap, and cap, PVC you will need to extend the sewer vents and all the roof boots should have been figured out, bought and on site before starting the roof. Not a whole lot of places may stock what your going to need.
If that pipe for the vent is round then you need a mushroom cap.
A rain cap is a piece that goes arounfd the pipe to devert the rain from running down the side of the pipe and getting in under the roof boot.
Metal roof takes a special type of boot a good one will have a metal band around the outside where the screws go. HD and Lowes do not sell them.