yup, those are the secondaries. the duratec V6 have primary and secondary ports. The secondaries stay closed until about 3800 rpm to make low end tq and then open up.
Heres a pic to better illustrate what were talking about:
Jim Hahn
1996 T-Red Contour SE Reborn 4/6/04
3.0L swap and Arizona Dyno Chip Turbo Kit
364 whp, 410 wtq @ 4,700 rpm