The 2003-2007 BD-Power Exhaust Pulse Manifold will fit the 6.7L, but not as a stock replacement. (The 5.9L manifold is often used when the DPF, EGR & VGT have been disabled and the turbo is upgraded.)
BD item # BD1045980 will fit the 88-98 12V Cummins Pickups.
Stainless is better beings it will not crack, but most aftermarket cast iron manifolds are jointed in separate locations to allow expansion and contractions. This eliminates the common issue with cast iron manifolds cracking.
Most of the exhaust manifolds on our site are designed with the stock flange for the stock turbo, unless otherwise noted. We do actually offer T4 manifolds for your truck though. They are designed specifically for turbo swaps like the one you're doing. You can find them here: http://www.xtremediesel.com/exhaust-m...