The culprit is mostly the EGR. You can't really do anything about it. SVTs come with a teflon coating on the TB inside which cuts down on deposits but doesn't eliminate them.
What does the tune-up include? If it's plugs, air and fuel filters, and the TB cleaning, the price doesn't actually sound that bad (as far as service goes). But before you spend $300, try cleaning the TB and combustion chambers with ford's spray cleaner. It's $7 and an hour of your time.
