Are you sure the upper you got is an authentic prototype part?
It strikes me that it wouldn't be too hard of a modification to do, which would explain the refinish as well as the fairly late upper.
IMHO, if I were wanting to build as close to the M16A1E1 as I could, I would get an RRA 9MM A2 upper and send it to one of our lovely Retro Forum "in house" machinists to get the gas tube clover leaf drilled, as well as the rear sight hole.
Then I would build the case deflector out of what it was made of - as far as I can tell, the pictured one is not milled, but Bondo, on the upper without the case deflector you can see the outline of where the bump was removed and/or fell off.
I'd use the prototype barrel you've got.
Per Lt. Col. Lutz when the A2 came up, he "designed" the modern A2 windage knob by chucking the picture knob in a drill and knocking off the corners - I'm not sure what the best solution would be, but just some trivia...
I'd probably just go with a Rapidex, but I suppose you could try to "build up" the corners of a standard knob, or once again, have a custom part made based on the A2 knob.
I'd stick with the barrel you've got, and otherwise build what you've got pictured - A1 lower, A1 ejection port cover, and teardrop forward assist, or possibly a "full" big button if you can find one.
I'd also look into the thread with Lt. Col. Lutz that I talked about, and take a look at his description of the prototype A2 grips and try to make one of those.
I'd also do the Type E stock and A2 buttplate.
Just make sure you use a peel washer to time the A2 comp.
ETA: The very Retro-ish A2 thread for those who have not seen it:
http://www.ar15.com/forums/t_3_118/626884_Why_did_the_military_go_from_the_A1_pistol_grip_to_the_A2_pistol_grip_.html&page=1
Colt "memento" for Lt. Col. Lutz:
~Augee