You could make it work, yes. Would it look right? I don't Beleive so. The cobras had different fenders than our four eyed cars. Not sure if this would make the fitment look rather odd. Not to mention, the cobra bumpers are made to flow into the cobra fender moldings, which obviously you don't have. It wouldn't look right to me, just my .02 cents.
IMO keep the four eyed front end. Everybody and their brother gets rid of the four eyed front ends for the aero look. Of course it's your own car, but this is happening way too much.
1986 GT with the typical poor boy mods. 3.73s, Hurst short throw, King Cobra Clutch with aluminum quadrant, lowered two inches on Eibach springs, Hopefully adding some heads and a decent intake soon!