Front derailleur will not sit properly on large cog without chain rub
You say you replaced the the derailleurs, crankset, brifters and pedals, but not the bottom bracket.  

My initial thought is that your crank is too far outboard because it requires a shorter bottom bracket axle than your previous crank.

The location of the square taper hole relative to the rings is different for different cranks, so different axle lengths are required to get the correct chain line (distance middle ring from center plane if the frame).

In your first picture the distance between the cranks and bracket shell does appear to be quite large.