welcome to fordtough.ca
"1. what is that green cylinder mounted on the exhaust? vibration tuner maybe?"
your correct in they use this to minimise exhaust vibrations for nvh.
"2. whats with the ugly alien looking intake with all its extra chambers? is this performance enhancing or just to minimize the howl of inrushing air when under hard acceleration? can i just replace it with same diameter pipe?"
the intake is designed with extra chambers for resonance reduction,if you change it out for a cai you may notice a howl under throttle.
"3. why the hell did they build the exhaust with 2 -2.5 pipes feeding from headers/cats into a 2.5 inch y-pipe that then enlarges to 3 " just before the muffler/cat flange, then back down to 2.5 inches again untill muffler then dual tailpipes? whats the point of offering mandrel bent pipes from headers back if you choke flow off with smaller diameter portions of y pipe and exhaust pipe."
this was done to optimise backpressure and sound quality(it's ugly but it seems to work
"4. what are the little pump/prime looking dealies on rear brakes? something to help maintain or bleed brakes?"
first time i seen those on a new truck i wondered the same thing,it seems they are for nvh reduction from the brakes(leave it to design engineers to come up with wierd stuff!)
"6.is the 18 inch spare tire a good indication of the smallest winter tire n wheel combo i can get and still not rub the brakes?"
the 18"rim would be the cheapest way to go. as for your audio system questions i'll have to research the system for you.